FA2HTGS(1)						     NCBI Tools User's Manual							FA2HTGS(1)

NAME

       fa2htgs - formatter for high throughput genome sequencing project submissions

SYNOPSIS

       fa2htgs	[-]  [-6 str]  [-7 str]  [-A filename]	[-C str]  [-D]	[-L filename]  [-M str] [-N] [-O filename] [-P str] [-Q filename] [-S str]
       [-T filename] [-X] [-a str] [-b N] [-c str] [-d str] [-e filename]  [-f]  -g str  [-h str]  [-i filename]  [-k str]  [-l N]  [-m]  [-n str]
       [-o filename] [-p N] [-q] [-r str] -s str [-t filename] [-u] [-v] [-w] [-x str]

DESCRIPTION

       fa2htgs is a program used to generate Seq-submits (an ASN.1 sequence submission file) for high throughput genome sequencing projects.

       fa2htgs	will read a FASTA file (or an Ace Contig file with Phrap sequence quality values), a Sequin submission template file, (to get con-
       tact and citation information for the submission), and a series of command line arguments (see below).  This  program  will  then  combines
       these  information  to make a submission suitable for GenBank. Once you have generated your submission file, you need to follow the submis-
       sion protocol (see the README present on your FTP account or mailed out to your Center).

       fa2htgs is intended for the automation by scripts for bulk submission of unannotated genome sequence. It can easily be  extended  from  its
       current	simple	form  to allow more complicated processing.  A submission prepared with fa2htgs can also be read into Psequin(1), and then
       annotated more extensively.

       Questions and concerns about this processing protocol, or how to use this tool should be forwarded to <htgs@ncbi.nlm.nih.gov>.

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -6 str SP6 clone (e.g., Contig1,left)

       -7 str T7 clone (e.g., Contig2,right)

       -A filename
	      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.

       -C str Clone library name (will appear as /clone-lib="str" on the source feature)

       -D     HTGS_DRAFT sequence

       -L filename
	      Read phrap contig order from filename.  This is a tab-delimited file that can be used to drive the order of contigs (normally speci-
	      fied 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.

       -M str Map name (will appear as /map="str" on the source feature)

       -N     Annotate assembly_fragments

       -O filename
	      Read comment from filename (100-character-per-line maximum; ~ is a linebreak and `~ is a literal ~.  You can check the  format  with
	      PSequin(1).)

       -P str 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"

       -Q filename
	      Read quality scores from filename

       -S str Strain name

       -T filename
	      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.)  Other-
	      wise, the coordinates are on the individual accessions, which need not start at base 1 of the record.

       -a str GenBank accession; use if and only if updating a sequence.

       -b N   Gap length (default = 100; anything from 0 to 1000000000 is legal)

       -c str Clone name (will appear as /clone in the source feature; can be the same as -s)

       -d str Title for sequence (will appear in GenBank DEFINITION line)

       -e filename
	      Log errors to filename

       -f     htgs_fulltop keyword

       -g str Genome Center tag (probably the same as your login name on the NCBI FTP server)

       -h str Chromosome (will appear as /chromosome in the source feature)

       -i filename
	      Filename for fasta input (default is stdin; mutually exclusive with -A and -T)

       -k str Add the supplied string as a keyword.

       -l N   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 pro-
	      vided 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

       -n str Organism name (default = Homo sapiens)

       -o filename
	      Filename for asn.1 output (default = stdout)

       -p N   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

       -r str Remark for update (brief comment describing the nature of the update, such as "new sequence", "new citation", or "updated features")

       -s str 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.

       -t filename
	      Filename for Seq-submit template (default = template.sub)

       -u     Take biosource from template

       -v     htgs_activefin keyword

       -w     Whole Genome Shotgun flag

       -x str 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  sec-
	      ondary.	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.

	      GREAT CARE 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.

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       Psequin(1), /usr/share/doc/ncbi-tools-bin/README.fa2htgs.gz

NCBI
								    2006-05-29								FA2HTGS(1)