A summary of options is included below.
- Print usage message
-6str SP6 clone (e.g., Contig1,left)
-7str T7 clone (e.g., Contig2,right)
-Afilename
Filename for accession list input (mutually exclusive with -T and -i). The input file contains a
tab-delimited table with three to five columns, which are accession number, start position, stop
position, and (optionally) length and strand. If start > stop, the minus strand on the referenced
accession is used. A gap is indicated by the word "gap" instead of an accession, 0 for the start
and stop positions, and a number for the length.
-Cstr Clone library name (will appear as /clone-lib="str" on the source feature)
-D HTGS_DRAFT sequence
-Lfilename
Read phrap contig order from filename. This is a tab-delimited file that can be used to drive the
order of contigs (normally specified by -P), as well as indicating the SP6 and T7 ends. It can
also be used when contigs are known to be in opposite orientation. For example:
Contig2 + 1 SP6 left
Contig3 + 1
Contig1 - T7 right
The first column is the contig name, the second is the orientation, the third is the
fragment_group, the fourth indicates the SP6 or T7 end, and the fifth says which side of SP6 or T7
end had vector removed.
-Mstr Map name (will appear as /map="str" on the source feature)
-N Annotate assembly_fragments
-Ofilename
Read comment from filename (100-character-per-line maximum; ~ is a linebreak and `~ is a literal
~. You can check the format with PSequin(1).)
-Pstr Contigs to use, separated by commas. If -P is not indicated with the -T option, then the
fragments will go in in the order that they are in the ace file (which is appropriate for a phase
1 record, but not for a phase 2 or 3). If you need to set the order of the segments of the ace
file, you need to set it with the -P flag, like this: -P"Contig1,Contig4,Contig3,Contig2,Contig5"-Qfilename
Read quality scores from filename-Sstr Strain name
-Tfilename
Filename for phrap input (mutually exclusive with -A and -i)
-X The coordinates in the input file are on the resulting segmented sequence. (Bases 1 through n of
each accession are used.) Otherwise, the coordinates are on the individual accessions, which need
not start at base 1 of the record.
-astr GenBank accession; use if and only if updating a sequence.
-bN Gap length (default = 100; anything from 0 to 1000000000 is legal)
-cstr Clone name (will appear as /clone in the source feature; can be the same as -s)
-dstr Title for sequence (will appear in GenBank DEFINITION line)
-efilename
Log errors to filename-f htgs_fulltop keyword
-gstr Genome Center tag (probably the same as your login name on the NCBI FTP server)
-hstr Chromosome (will appear as /chromosome in the source feature)
-ifilename
Filename for fasta input (default is stdin; mutually exclusive with -A and -T)
-kstr Add the supplied string as a keyword.
-lN Length of sequence in bp (default = 0). The length is checked against the actual number of bases
we get. For phase 1 and 2 sequence it is also used to estimate gap lengths. For phase 1 and 2
records, it is important to use a number GREATER than the amount of provided nucleotide, otherwise
this will generate false `gaps'. Here is assumed that the putative full length of the BAC or
cosmid will be used. There should be at least 20 to 30 `n' in between the segments (you can check
for these in Sequin), as this will ensure proper behavior when this sequence is used with BLAST.
Otherwise `artifactual' unrelated segment neighbors may be brought into proximity of each other.
-m Take comment from template
-nstr Organism name (default = Homo sapiens)
-ofilename
Filename for asn.1 output (default = stdout)
-pN HTGS phase:
1 A collection of unordered contigs with gaps of unknown length. A Phase 1 record must at
the very least have two segments with one gap. (default)
2 A series of ordered contigs, possibly with known gap lengths. This could be a single
sequence without gaps, if the sequence has ambiguities to resolve.
3 A single contiguous sequence. This sequence is finished, but not necessarily annotated.
-q htgs_cancelled keyword
-rstr Remark for update (brief comment describing the nature of the update, such as "new sequence", "new
citation", or "updated features")
-sstr Sequence name. The sequence must have a name that is unique within the genome center. We use the
combination of the genome center name (-g argument) and the sequence name (-s) to track this
sequence and to talk to you about it. The name can have any form you like but must be unique
within your center.
-tfilename
Filename for Seq-submit template (default = template.sub)
-u Take biosource from template
-v htgs_activefin keyword
-w Whole Genome Shotgun flag
-xstr Secondary accession numbers, separated by commas, s.t. U10000,L11000.
In some cases a large segment will supersede another or group of other accession numbers
(records). These records which are no longer wanted in GenBank should be made secondary. Using
the -x argument you can list the Accession Numbers you want to make secondary. This will instruct
us to remove the accession number(s) from GenBank, and will no longer be part of the GenBank
release. They will nonetheless be available from Entrez.
GREATCARE should be taken when using this argument!!! Improper use of accession numbers here
will result in the inappropriate withdrawal of GenBank records from GenBank, EMBL and DDBJ. We
provide this parameter as a convenience to submitting centers, but this may need to be removed if
it is not used carefully.
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