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- Committer: Package Import Robot
- Author(s): Andreas Tille
- Date: 2012-05-21 21:56:38 UTC
- mfrom: (1.1.2)
- Revision ID: package-import@ubuntu.com-20120521215638-pqynm387yv9cujk1
Tags: 1.1.5-1
* New upstream version fixing the FTBFS with gcc-4.7 bug
Closes: #667214
* debian/patches/fix-unused-but-set-variable.patch: Removed
because applied upstream
Closes: #667214
* debian/patches/fix-unused-but-set-variable.patch: Removed
because applied upstream
- files added:
- jellyfish/dna_codes.cc
- files removed:
- .pc/fix-unused-but-set-variable.patch
- .pc/fix-unused-but-set-variable.patch/unit_tests
- files modified:
- .pc/applied-patches
added
removed
.pc/man/doc/jellyfish.man
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'\" t
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.\" Manual page created with latex2man on Sat Apr 23 05:39:15 EDT 2011
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.\" Manual page created with latex2man on Wed Feb 29 10:58:48 EST 2012
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.\" NOTE: This file is generated, DO NOT EDIT.
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.de Vb
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.ft CW
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.br
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jellyfish query
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\fIhash\fP
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.br
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jellyfish cite
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.br
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.PP
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Plus equivalent version for Quake
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mode: qhisto,
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qdump
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and qmerge\&.
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.PP
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.SH DESCRIPTION
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is a k\-mer counter based on a multi\-threaded hash
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table implementation.
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.PP
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.SS COUNTING AND MERGING
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.PP
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To count k\-mers, use a command like:
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.PP
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.Vb
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jellyfish count \-m 22 \-o output \-c 3 \-s 10000000 \-t 32 input.fasta
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.Ve
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.PP
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This will count the the 22\-mers in species.fasta with 32 threads. The
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This will count the the 22\-mers in input.fasta with 32 threads. The
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counter field in the hash uses only 3 bits and the hash has at least
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10 million entries. Let the size of the table be s=2^l and the max
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reprobe value is less than 2^r, then the memory usage per entry in
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the hash is (in bits, not bytes) 2k\-l+r+1\&.
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.PP
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10 million entries.
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.PP
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The output files will be named output_0, output_1, etc. (the prefix
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is specified with the \fB\-o\fP
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switch). If the hash is large enough
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(has specified by the \fB\-s\fP
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switch) to fit all the k\-mers, there
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will be only one output file named output_0. If the hash filled up
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before all the mers were read, the hash is dumped to disk, zeroed out
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and reading in mers resumes. Multiple intermediary files will be
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present on the disks, named output_0, output_1, etc.
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.PP
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To obtain correct results from the other sub\-commands (such as histo,
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stats, etc.), the multiple output files, if any, need to be merged into one
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with the merge command. For example with the following command:
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.PP
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.Vb
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jellyfish merge \-o output.jf output\\_*
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.Ve
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.PP
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Should you get many intermediary output files (say hundreds), the size
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of the hash table is too small. Rerunning Jellyfish
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with a
100
larger size (option \fB\-s\fP)
101
is probably faster than merging all the
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intermediary files.
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.PP
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.SS ORIENTATION
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When the orientation of the sequences in the input fasta file is not
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known, e.g. in sequencing reads, using \fB--both\-strands\fP
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(\fB\-C\fP)
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makes the most sense.
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.PP
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For any k\-mer m, its canonical representation is m itself or its
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reverse\-complement, whichever comes first lexicographically. With the
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option \fB\-C\fP,
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only the canonical representation of the mers are
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stored in the hash and the count value is the number of occurrences of
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both the mer and its reverse\-complement.
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.PP
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.SS CHOOSING THE HASH SIZE
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.PP
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To achieve the best performance, a minimum number of intermediary
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files should be written to disk. So the parameter \fB\-s\fP
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should be
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chosen to fit as many k\-mers as possible (ideally all of them) while
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still fitting in memory.
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.PP
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We consider to examples: counting mers in sequencing reads and in a
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finished genome.
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.PP
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First, suppose we count k\-mers in short sequencing reads:
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there are n reads and there is an average of 1 error per reads where
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each error generates k unique mers. If the genome size is G, the
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size of the hash (option \fB\-s\fP)
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to fit all k\-mers at once is estimated to: $(G +
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k*n)/0.8$. The division by 0.8 compensates for the maximum usage of
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approximately $80%$ of the hash table.
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.PP
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On the other hand, when counting k\-mers in an assembled sequence of
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length G, setting \fB\-s\fP
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to G is appropriate.
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.PP
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As a matter of convenience, Jellyfish understands ISO suffixes for the
141
size of the hash. Hence \&'\-s 10M\&' stands 10 million entries while \&'\-s
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50G\&' stands for 50 billion entries.
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.PP
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The actual memory usage of the hash table can be computed as
145
follow. The actual size of the hash will be rounded up to the next
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power of 2: s=2^l\&. The parameter r is such that the maximum
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reprobe value (\fB\-p\fP)
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plus one is less than 2^r\&. Then the memory usage per
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entry in the hash is (in bits, not bytes) 2k\-l+r+1\&. The total memory
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usage of the hash table in bytes is: 2^l*(2k\-l+r+1)/8\&.
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.PP
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.SS CHOOSING THE COUNTING FIELD SIZE
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To save space, the hash table supports variable length counter, i.e. a
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k\-mer occurring only a few times will use a small counter, a k\-mer
73
occurring many times will used multiple entries in the hash. The
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\fB\-c\fP
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specify the length of the small counter. The tradeoff is: a
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low value will save space per entry in the hash but will increase the
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number of entries used, hence maybe requiring a larger hash. In
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practice, use a value for \fB\-c\fP
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occurring many times will used multiple entries in the hash.
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.PP
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Important: the size of the couting field does NOT change the result,
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it only impacts the amount of memory used. In particular, there is no
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maximum value in the hash. Even if the counting field uses 5 bits, a
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k\-mer occuring 2 million times will have a value reported of 2
161
million (i.e., it is not capped at 2^5).
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.PP
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The \fB\-c\fP
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specify the length (in bits) of the counting field. The
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trade off is as follows: a low value will save space per entry in the
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hash but can potentially increase the number of entries used, hence
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maybe requiring a larger hash.
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.PP
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In practice, use a value for \fB\-c\fP
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so that most of you k\-mers
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require only 1 entry. For example, to count k\-mers in a genome,
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where most of the sequence is unique, use \fB\-c\fP\fI1\fP
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or
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\fB\-c\fP\fI2\fP\&.
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For sequencing reads, use a value for
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\fB\-c\fP
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large enough to counts up to twice the coverage.
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.PP
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When the orientation of the sequences in the input fasta file is not
89
known, e.g. in sequencing reads, using \fB--both\-strands\fP
90
(\fB\-C\fP)
91
makes the most sense.
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.PP
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The following subcommand are used to look at the result: histo, dump, stats.
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.PP
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.SH OPTIONS
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For sequencing reads, use a value for \fB\-c\fP
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large
177
enough to counts up to twice the coverage. For example, if the
178
coverage is 10X, choose a counter length of 5 (\fB\-c\fP\fI5\fP)
179
as $2^5 > 20$.
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.PP
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.SH SUBCOMMANDS AND OPTIONS
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182
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183
.SS COUNT
184
Usage: jellyfish count [options] file:path+
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185
.PP
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186
Count k\-mers or qmers in fasta or fastq files
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.PP
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Usage: jellyfish count [OPTIONS]... [file.f[aq]]...
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.PP
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.TP
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\fB\-h\fP,\fB--help\fP
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Print help and exit
106
.TP
107
\fB--full\-help\fP
108
Print help, including hidden options, and exit
109
.TP
110
\fB\-V\fP,\fB--version\fP
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Print version and exit
188
Options (default value in (), *required):
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.TP
113
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\fB\-m\fP,
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\fB--mer\-len\fP\fI=INT\fP
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Length of mer (mandatory)
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\fB--mer\-len\fP\fI=uint32\fP
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*Length of mer
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.TP
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\fB\-s\fP,
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\fB--size\fP\fI=LONG\fP
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Hash size (mandatory)
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\fB--size\fP\fI=uint64\fP
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*Hash size
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.TP
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\fB\-t\fP,
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\fB--threads\fP\fI=INT\fP
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Number of threads (default=1)
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\fB--threads\fP\fI=uint32\fP
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Number of threads (1)
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.TP
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\fB\-o\fP,
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\fB--output\fP\fI=STRING\fP
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Output prefix (default=mer_counts)
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\fB--output\fP\fI=string\fP
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Output prefix (mer_counts)
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.TP
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\fB\-c\fP,
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\fB--counter\-len\fP\fI=Length\fP
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in bits
132
Length of counting field (default=7)
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in bits Length of counting field (7)
133
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.TP
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\fB--out\-counter\-len\fP\fI=Length\fP
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in bytes
136
Length of counter field in output
137
(default=4)
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in bytes Length of counter field in output (4)
138
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.TP
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\fB\-C\fP,\fB--both\-strands\fP
140
Count both strand, canonical representation
141
(default=off)
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Count both strand, canonical representation (false)
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.TP
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\fB\-p\fP,
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\fB--reprobes\fP\fI=INT\fP
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Maximum number of reprobes (default=62)
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\fB--reprobes\fP\fI=uint32\fP
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Maximum number of reprobes (62)
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.TP
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\fB\-r\fP,\fB--raw\fP
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Write raw database (default=off)
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Write raw database (false)
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.TP
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\fB\-q\fP,\fB--quake\fP
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Quake compatibility mode (default=off)
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.TP
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\fB--quality\-start\fP\fI=INT\fP
154
Starting ASCII for quality values
155
(default=64)
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.TP
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\fB--min\-quality\fP\fI=INT\fP
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Minimum quality. A base with lesser quality
159
becomes an N (default=0)
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Quake compatibility mode (false)
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.TP
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\fB--quality\-start\fP\fI=uint32\fP
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Starting ASCII for quality values (64)
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.TP
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\fB--min\-quality\fP\fI=uint32\fP
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Minimum quality. A base with lesser quality becomes an N (0)
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.TP
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\fB\-L\fP,
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\fB--lower\-count\fP\fI=LONG\fP
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\fB--lower\-count\fP\fI=uint64\fP
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Don\&'t output k\-mer with count < lower\-count
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.TP
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\fB\-U\fP,
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\fB--upper\-count\fP\fI=LONG\fP
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\fB--upper\-count\fP\fI=uint64\fP
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Don\&'t output k\-mer with count > upper\-count
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.TP
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\fB--matrix\fP\fI=Matrix\fP
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.TP
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\fB--timing\fP\fI=Timing\fP
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file Print timing information
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.TP
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\fB--stats\fP\fI=Stats\fP
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file Print stats
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.TP
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\fB--usage\fP
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Usage
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.TP
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\fB\-h\fP,\fB--help\fP
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This message
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.TP
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\fB--full\-help\fP
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Detailed help
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.TP
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\fB\-V\fP,\fB--version\fP
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Version
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.PP
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.SS STATS
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Usage: jellyfish stats [options] db:path
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.PP
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Statistics
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.PP
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Display some statistics about the k\-mers in the hash:
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.PP
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Unique: Number of k\-mers which occur only once.
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Distinct: Number of k\-mers, not counting multiplicity.
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Total: Number of k\-mers, including multiplicity.
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Max_count: Maximum number of occurrence of a k\-mer.
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.PP
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Options (default value in (), *required):
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.TP
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\fB\-L\fP,
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\fB--lower\-count\fP\fI=uint64\fP
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Don\&'t consider k\-mer with count < lower\-count
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.TP
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\fB\-U\fP,
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\fB--upper\-count\fP\fI=uint64\fP
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Don\&'t consider k\-mer with count > upper\-count
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.TP
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\fB\-v\fP,\fB--verbose\fP
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Verbose (false)
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.TP
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\fB\-o\fP,
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\fB--output\fP\fI=string\fP
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Output file
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.TP
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\fB--usage\fP
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Usage
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.TP
293
\fB\-h\fP,\fB--help\fP
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This message
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.TP
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\fB--full\-help\fP
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Detailed help
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.TP
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\fB\-V\fP,\fB--version\fP
300
Version
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.PP
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302
.SS HISTO
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Usage: jellyfish histo [options] db:path
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.PP
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Create an histogram of k\-mer occurrences
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.PP
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Usage: jellyfish histo [OPTIONS]... [database.jf]...
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.PP
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.TP
182
\fB--help\fP
183
Print help and exit
184
.TP
185
\fB\-V\fP,\fB--version\fP
186
Print version and exit
187
.TP
188
\fB\-s\fP,
189
\fB--buffer\-size\fP\fI=Buffer\fP
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length
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Length in bytes of input buffer
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(default=10000000)
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Create an histogram with the number of k\-mers having a given
308
count. In bucket \&'i\&' are tallied the k\-mers which have a count \&'c\&'
309
satisfying \&'low+i*inc <= c < low+(i+1)*inc\&'\&. Buckets in the output are
310
labeled by the low end point (low+i*inc).
311
.PP
312
The last bucket in the output behaves as a catchall: it tallies all
313
k\-mers with a count greater or equal to the low end point of this
314
bucket.
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.PP
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Options (default value in (), *required):
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.TP
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318
\fB\-l\fP,
195
\fB--low\fP\fI=LONG\fP
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Low count value of histogram (default=1)
319
\fB--low\fP\fI=uint64\fP
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Low count value of histogram (1)
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.TP
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\fB\-h\fP,
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\fB--high\fP\fI=LONG\fP
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High count value of histogram
201
(default=10000)
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\fB--high\fP\fI=uint64\fP
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High count value of histogram (10000)
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.TP
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\fB\-i\fP,
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\fB--increment\fP\fI=LONG\fP
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Increment value for buckets (default=1)
327
\fB--increment\fP\fI=uint64\fP
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Increment value for buckets (1)
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.TP
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\fB\-t\fP,
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\fB--threads\fP\fI=INT\fP
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Number of threads (default=1)
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\fB--threads\fP\fI=uint32\fP
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Number of threads (1)
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.TP
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\fB\-f\fP,\fB--full\fP
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Full histo. Don\&'t skip count 0. (false)
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.TP
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\fB\-o\fP,
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\fB--output\fP\fI=STRING\fP
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Output file (default=/dev/fd/1)
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\fB--output\fP\fI=string\fP
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Output file
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.TP
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\fB\-v\fP,\fB--verbose\fP
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Output information (false)
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.TP
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\fB--usage\fP
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Usage
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.TP
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\fB--help\fP
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This message
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.TP
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\fB--full\-help\fP
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Detailed help
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.TP
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\fB\-V\fP,\fB--version\fP
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Version
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.PP
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.SS DUMP
357
Usage: jellyfish dump [options] db:path
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.PP
217
359
Dump k\-mer counts
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.PP
219
Usage: jellyfish stats [OPTIONS]... [database.jf]...
361
By default, dump in a fasta format where the header is the count and
362
the sequence is the sequence of the k\-mer. The column format is a 2
363
column output: k\-mer count.
220
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.PP
221
.TP
222
\fB\-h\fP,\fB--help\fP
223
Print help and exit
224
.TP
225
\fB\-V\fP,\fB--version\fP
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Print version and exit
365
Options (default value in (), *required):
227
366
.TP
228
367
\fB\-c\fP,\fB--column\fP
229
Column format (default=off)
368
Column format (false)
230
369
.TP
231
370
\fB\-t\fP,\fB--tab\fP
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Tab separator (default=off)
371
Tab separator (false)
233
372
.TP
234
373
\fB\-L\fP,
235
\fB--lower\-count\fP\fI=LONG\fP
374
\fB--lower\-count\fP\fI=uint64\fP
236
375
Don\&'t output k\-mer with count < lower\-count
237
376
.TP
238
377
\fB\-U\fP,
239
\fB--upper\-count\fP\fI=LONG\fP
378
\fB--upper\-count\fP\fI=uint64\fP
240
379
Don\&'t output k\-mer with count > upper\-count
241
380
.TP
242
381
\fB\-o\fP,
243
\fB--output\fP\fI=STRING\fP
244
Output file (default=/dev/fd/1)
245
.PP
246
.SS STATS
247
.PP
248
Statistics
249
.PP
250
Usage: jellyfish stats [OPTIONS]... [database.jf]...
251
.PP
382
\fB--output\fP\fI=string\fP
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Output file
384
.TP
385
\fB--usage\fP
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Usage
252
387
.TP
253
388
\fB\-h\fP,\fB--help\fP
254
Print help and exit
255
.TP
256
\fB--full\-help\fP
257
Print help, including hidden options, and exit
389
This message
258
390
.TP
259
391
\fB\-V\fP,\fB--version\fP
260
Print version and exit
261
.TP
262
\fB\-L\fP,
263
\fB--lower\-count\fP\fI=LONG\fP
264
Don\&'t output k\-mer with count < lower\-count
265
.TP
266
\fB\-U\fP,
267
\fB--upper\-count\fP\fI=LONG\fP
268
Don\&'t output k\-mer with count > upper\-count
269
.TP
270
\fB\-v\fP,\fB--verbose\fP
271
Verbose (default=off)
272
.TP
273
\fB\-o\fP,
274
\fB--output\fP\fI=STRING\fP
275
Output file (default=/dev/fd/1)
392
Version
276
393
.PP
277
394
.SS MERGE
395
Usage: jellyfish merge [options] input:string+
278
396
.PP
279
397
Merge jellyfish databases
280
398
.PP
281
Usage: jellyfish merge [OPTIONS]... [database.jf]...
282
.PP
283
.TP
284
\fB\-h\fP,\fB--help\fP
285
Print help and exit
286
.TP
287
\fB\-V\fP,\fB--version\fP
288
Print version and exit
399
Options (default value in (), *required):
289
400
.TP
290
401
\fB\-s\fP,
291
402
\fB--buffer\-size\fP\fI=Buffer\fP
292
length
293
Length in bytes of input buffer
294
(default=10000000)
295
.TP
296
\fB\-o\fP,
297
\fB--output\fP\fI=STRING\fP
298
Output file (default=mer_counts_merged.jf)
299
.TP
300
\fB--out\-counter\-len\fP\fI=INT\fP
301
Length (in bytes) of counting field in output
302
(default=4)
303
.TP
304
\fB--out\-buffer\-size\fP\fI=LONG\fP
305
Size of output buffer per thread
306
(default=10000000)
307
.TP
308
\fB\-v\fP,\fB--verbose\fP
309
Be verbose (default=off)
403
length Length in bytes of input buffer (10000000)
404
.TP
405
\fB\-o\fP,
406
\fB--output\fP\fI=string\fP
407
Output file (mer_counts_merged.jf)
408
.TP
409
\fB--out\-counter\-len\fP\fI=uint32\fP
410
Length (in bytes) of counting field in output (4)
411
.TP
412
\fB--out\-buffer\-size\fP\fI=uint64\fP
413
Size of output buffer per thread (10000000)
414
.TP
415
\fB\-v\fP,\fB--verbose\fP
416
Be verbose (false)
417
.TP
418
\fB--usage\fP
419
Usage
420
.TP
421
\fB\-h\fP,\fB--help\fP
422
This message
423
.TP
424
\fB\-V\fP,\fB--version\fP
425
Version
426
.PP
427
.SS QUERY
428
Usage: jellyfish query [options] db:path
429
.PP
430
Query from a compacted database
431
.PP
432
Query a hash. It reads k\-mers from the standard input and write the counts on the standard output.
433
.PP
434
Options (default value in (), *required):
435
.TP
436
\fB\-C\fP,\fB--both\-strands\fP
437
Both strands (false)
438
.TP
439
\fB\-c\fP,\fB--cary\-bit\fP
440
Value field as the cary bit information (false)
441
.TP
442
\fB\-i\fP,
443
\fB--input\fP\fI=file\fP
444
Input file
445
.TP
446
\fB\-o\fP,
447
\fB--output\fP\fI=file\fP
448
Output file
449
.TP
450
\fB--usage\fP
451
Usage
452
.TP
453
\fB\-h\fP,\fB--help\fP
454
This message
455
.TP
456
\fB\-V\fP,\fB--version\fP
457
Version
458
.PP
459
.SS QHISTO
460
Usage: jellyfish qhisto [options] db:string
461
.PP
462
Create an histogram of k\-mer occurences
463
.PP
464
Options (default value in (), *required):
465
.TP
466
\fB\-l\fP,
467
\fB--low\fP\fI=double\fP
468
Low count value of histogram (0.0)
469
.TP
470
\fB\-h\fP,
471
\fB--high\fP\fI=double\fP
472
High count value of histogram (10000.0)
473
.TP
474
\fB\-i\fP,
475
\fB--increment\fP\fI=double\fP
476
Increment value for buckets (1.0)
477
.TP
478
\fB\-f\fP,\fB--full\fP
479
Full histo. Don\&'t skip count 0. (false)
480
.TP
481
\fB--usage\fP
482
Usage
483
.TP
484
\fB--help\fP
485
This message
486
.TP
487
\fB\-V\fP,\fB--version\fP
488
Version
489
.PP
490
.SS QDUMP
491
Usage: jellyfish qdump [options] db:path
492
.PP
493
Dump k\-mer from a qmer database
494
.PP
495
By default, dump in a fasta format where the header is the count and
496
the sequence is the sequence of the k\-mer. The column format is a 2
497
column output: k\-mer count.
498
.PP
499
Options (default value in (), *required):
500
.TP
501
\fB\-c\fP,\fB--column\fP
502
Column format (false)
503
.TP
504
\fB\-t\fP,\fB--tab\fP
505
Tab separator (false)
506
.TP
507
\fB\-L\fP,
508
\fB--lower\-count\fP\fI=double\fP
509
Don\&'t output k\-mer with count < lower\-count
510
.TP
511
\fB\-U\fP,
512
\fB--upper\-count\fP\fI=double\fP
513
Don\&'t output k\-mer with count > upper\-count
514
.TP
515
\fB\-v\fP,\fB--verbose\fP
516
Be verbose (false)
517
.TP
518
\fB\-o\fP,
519
\fB--output\fP\fI=string\fP
520
Output file
521
.TP
522
\fB--usage\fP
523
Usage
524
.TP
525
\fB\-h\fP,\fB--help\fP
526
This message
527
.TP
528
\fB\-V\fP,\fB--version\fP
529
Version
530
.PP
531
.SS QMERGE
532
Usage: jellyfish merge [options] db:string+
533
.PP
534
Merge quake databases
535
.PP
536
Options (default value in (), *required):
537
.TP
538
\fB\-s\fP,
539
\fB--size\fP\fI=uint64\fP
540
*Merged hash table size
541
.TP
542
\fB\-m\fP,
543
\fB--mer\-len\fP\fI=uint32\fP
544
*Mer length
545
.TP
546
\fB\-o\fP,
547
\fB--output\fP\fI=string\fP
548
Output file (merged.jf)
549
.TP
550
\fB\-p\fP,
551
\fB--reprobes\fP\fI=uint32\fP
552
Maximum number of reprobes (62)
553
.TP
554
\fB--usage\fP
555
Usage
556
.TP
557
\fB\-h\fP,\fB--help\fP
558
This message
559
.TP
560
\fB--full\-help\fP
561
Detailed help
562
.TP
563
\fB\-V\fP,\fB--version\fP
564
Version
310
565
.PP
311
566
.SS CITE
567
Usage: jellyfish cite [options]
312
568
.PP
313
569
How to cite Jellyfish\&'s paper
314
570
.PP
315
Usage: jellyfish cite [OPTIONS]...
571
Citation of paper
316
572
.PP
317
.TP
318
\fB\-h\fP,\fB--help\fP
319
Print help and exit
320
.TP
321
\fB\-V\fP,\fB--version\fP
322
Print version and exit
573
Options (default value in (), *required):
323
574
.TP
324
575
\fB\-b\fP,\fB--bibtex\fP
325
Bibtex format (default=off)
576
Bibtex format (false)
326
577
.TP
327
578
\fB\-o\fP,
328
\fB--output\fP\fI=STRING\fP
329
Output file (default=/dev/fd/1)
579
\fB--output\fP\fI=string\fP
580
Output file
581
.TP
582
\fB--usage\fP
583
Usage
584
.TP
585
\fB\-h\fP,\fB--help\fP
586
This message
587
.TP
588
\fB\-V\fP,\fB--version\fP
589
Version
330
590
.PP
331
591
.SH VERSION
332
592
333
593
.PP
334
Version: 1.1 of 2010/10/1
594
Version: 1.1.4 of 2010/10/1
335
595
.PP
336
596
.SH BUGS
337
597
338
598
.PP
339
599
.TP
340
600
.B *
341
jellyfish merge has not been parallelized and is very
342
slow.
601
jellyfish merge has not been parallelized and is
602
relatively slow.
603
.TP
604
.B *
605
The hash table does not grow in memory automatically and
606
jellyfish merge
607
is not called automatically on the
608
intermediary files (if any).
343
609
.PP
344
610
.SH COPYRIGHT & LICENSE
345
611
362
628
.br
363
629
You should have received a copy of the GNU General Public License
364
630
along with this program. If not, see
365
<\fBhttp://www.gnu.org/licenses/\fP>.
631
\fBhttp://www.gnu.org/licenses/\fP\&.
366
632
.PP
367
633
.SH AUTHORS
368
634
Loggerhead is a web-based interface for Breezy
Version: 2.0.1