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.TH FA2HTGS 1 2001-12-28 NCBI "NCBI Tools User's Manual"
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fa2htgs \- formatter for high throughput genome sequencing project submissions
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[\|\fB-6\fP\ \fIstr\fP\|]
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[\|\fB-7\fP\ \fIstr\fP\|]
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[\|\fB-A\fP\ \fIfilename\fP\|]
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[\|\fB-C\fP\ \fIstr\fP\|]
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[\|\fB-L\fP\ \fIfilename\fP\|]
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[\|\fB-M\fP\ \fIstr\fP\|]
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[\|\fB-O\fP\ \fIfilename\fP\|]
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[\|\fB-P\fP\ \fIstr\fP\|]
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[\|\fB-S\fP\ \fIstr\fP\|]
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[\|\fB-T\fP\ \fIfilename\fP\|]
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[\|\fB-a\fP\ \fIstr\fP\|]
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[\|\fB-b\fP\ \fIN\fP\|]
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[\|\fB-c\fP\ \fIstr\fP\|]
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[\|\fB-d\fP\ \fIstr\fP\|]
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[\|\fB-e\fP\ \fIfilename\fP\|]
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[\|\fB-h\fP\ \fIstr\fP\|]
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[\|\fB-i\fP\ \fIfilename\fP\|]
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[\|\fB-l\fP\ \fIN\fP\|]
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[\|\fB-n\fP\ \fIstr\fP\|]
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[\|\fB-o\fP\ \fIfilename\fP\|]
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[\|\fB-p\fP\ \fIN\fP\|]
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[\|\fB-r\fP\ \fIstr\fP\|]
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[\|\fB-t\fP\ \fIfilename\fP\|]
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[\|\fB-x\fP\ \fIstr\fP\|]
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This manual page documents briefly the \fBfa2htgs\fP command.
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This manual page was written for the Debian GNU/Linux distribution
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because the original program does not have a manual page.
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\fBfa2htgs\fP is a program used to generate Seq-submits (an ASN.1
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sequence submission file) for high throughput genome sequencing
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\fBfa2htgs\fP will read a FASTA file (or an Ace Contig file with Phrap
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sequence quality values), a Sequin submission template file, (to get
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contact and citation information for the submission), and a series of
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command line arguments (see below). This program will then combines
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these information to make a submission suitable for GenBank. Once you
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have generated your submission file, you need to follow the submission
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protocol (see the README present on your FTP account or mailed out to
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\fBfa2htgs\fP is intended for the automation by scripts for bulk
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submission of unannotated genome sequence. It can easily be extended
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from its current simple form to allow more complicated processing. A
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submission prepared with \fBfa2htgs\fP can also be read into
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\fBPsequin\fP(1), and then annotated more extensively.
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Questions and concerns about this processing protocol, or how to
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use this tool should be forwarded to <htgs@ncbi.nlm.nih.gov>.
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A summary of options is included below.
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SP6 clone (e.g., Contig1,left)
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T7 clone (e.g., Contig2,right)
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\fB-A\fP\ \fIfilename\fP
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Filename for accession list input (mutually exclusive with \fB-T\fP
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and \fB-i\fP). The input file contains a tab-delimited table with
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three to five columns, which are accession number, start position,
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stop position, and (optionally) length and strand. If start > stop,
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the minus strand on the referenced accession is used. A gap is
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indicated by the word "gap" instead of an accession, 0 for the start
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and stop positions, and a number for the length.
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Clone library name (will appear as \fB/clone-lib="\fP\fIstr\fP\fB"\fP
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on the source feature)
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\fB-L\fP\ \fIfilename\fP
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Read phrap contig order from \fIfilename\fP. This is a tab-delimited
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file that can be used to drive the order of contigs (normally
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specified by \fB-P\fP), as well as indicating the SP6 and T7 ends. It
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can also be used when contigs are known to be in opposite orientation.
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The first column is the contig name, the second is the orientation,
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the third is the fragment_group, the fourth indicates the SP6 or T7
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end, and the fifth says which side of SP6 or T7 end had vector
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Map name (will appear as \fB/map="\fP\fIstr\fP\fB"\fP on the source feature)
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Annotate assembly_fragments
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\fB-O\fP\ \fIfilename\fP
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Read comment from \fIfilename\fP (100-character-per-line maximum;
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\fB~\fP is a linebreak and \fB`~\fP is a literal \fB~\fP. You can
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check the format with \fBPSequin\fP(1).)
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Contigs to use, separated by commas. If \fB-P\fP is not indicated
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with the \fB-T\fP option, then the fragments will go in in the order
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that they are in the ace file (which is appropriate for a phase 1
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record, but not for a phase 2 or 3). If you need to set the order of
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the segments of the ace file, you need to set it with the \fB-P\fP
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flag, like this: \fB-P "Contig1,Contig4,Contig3,Contig2,Contig5"\fP
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\fB-T\fP\ \fIfilename\fP
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Filename for phrap input (mutually exclusive with \fB-A\fP and \fB-i\fP)
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The coordinates in the input file are on the resulting segmented
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sequence. (Bases 1 through \fIn\fP of each accession are used.)
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Otherwise, the coordinates are on the individual accessions, which
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need not start at base 1 of the record.
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GenBank accession; use if and only if updating a sequence.
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Gap length (default = 100; anything from 0 to 1000000000 is legal)
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Clone name (will appear as \fB/clone\fP in the source feature; can be
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the same as \fB-s\fP)
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Title for sequence (will appear in GenBank \fBDEFINITION\fP line)
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\fB-e\fP\ \fIfilename\fP
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Log errors to \fIfilename\fP
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Genome Center tag (probably the same as your login name on the NCBI FTP server)
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Chromosome (will appear as \fB/chromosome\fP in the source feature)
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\fB-i\fP\ \fIfilename\fP
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Filename for fasta input (default is stdin; mutually exclusive with
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\fB-A\fP and \fB-T\fP)
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Length of sequence in bp (default = 0). The length is checked against
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the actual number of bases we get. For phase 1 and 2 sequence it is
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also used to estimate gap lengths. For phase 1 and 2 records, it is
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important to use a number GREATER than the amount of provided
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nucleotide, otherwise this will generate false 'gaps'. Here is
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assumed that the putative full length of the BAC or cosmid will be
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used. There should be at least 20 to 30 'n' in between the segments
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(you can check for these in Sequin), as this will ensure proper
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behavior when this sequence is used with BLAST. Otherwise
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'artifactual' unrelated segment neighbors may be brought into
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proximity of each other.
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Take comment from template
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Organism name (default = Homo sapiens)
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\fB-o\fP\ \fIfilename\fP
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Filename for asn.1 output (default = stdout)
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A collection of unordered contigs with gaps of unknown length. A
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Phase 1 record must at the very least have two segments with one gap.
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A series of ordered contigs, possibly with known gap lengths. This
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could be a single sequence without gaps, if the sequence has
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ambiguities to resolve.
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A single contiguous sequence. This sequence is finished, but not
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necessarily annotated.
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htgs_cancelled keyword
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Remark for update (brief comment describing the nature of the update,
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such as "new sequence", "new citation", or "updated features")
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Sequence name. The sequence must have a name that is unique within
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the genome center. We use the combination of the genome center name
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(\fB-g\fP argument) and the sequence name (\fB-s\fP) to track this
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sequence and to talk to you about it. The name can have any form you
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like but must be unique within your center.
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\fB-t\fP\ \fIfilename\fP
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Filename for Seq-submit template (default = template.sub)
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Take biosource from template
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htgs_activefin keyword
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Secondary accession numbers, separated by commas, s.t. U10000,L11000.
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In some cases a large segment will supersede another or group of other
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accession numbers (records). These records which are no longer wanted
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in GenBank should be made secondary. Using the \fB-x\fP argument you
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can list the Accession Numbers you want to make secondary. This will
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instruct us to remove the accession number(s) from GenBank, and will
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no longer be part of the GenBank release. They will nonetheless be
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available from Entrez.
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\fBGREAT CARE\fP should be taken when using this argument!!! Improper
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use of accession numbers here will result in the inappropriate
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withdrawal of GenBank records from GenBank, EMBL and DDBJ. We provide
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this parameter as a convenience to submitting centers, but this may
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need removed if it is not used carefully.
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This manual page was written by Aaron M. Ucko <ucko@debian.org>,
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for the Debian GNU/Linux system (but may be used by others).
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/usr/share/doc/ncbi-tools-bin/README.fa2htgs.gz
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debian/man/fa2htgs.1
