assemble_contigs

Biopiece: assemble_contigs

Description

Do not confuse this Biopiece with assemble_tag_contigs.

assemble_contigs can be used to compile contigs from hits in the stream. These hits can be found by mapping reads to a reference genome using bowtie_seq or other mapping tools that output the following keys:

• STRAND
• S_ID
• Q_ID
• S_BEG
• S_END

or for mate-pair type hits:

• STRAND
• S_ID
• Q_ID1
• Q_ID2
• S_BEG1
• S_END1
• S_BEG2
• S_END2

The resulting contigs are composed of records like this:

CONTIG: 1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1
S_ID: contig00114
S_BEG: 20920
CONTIG_LEN: 18
CONTIG_MEAN: 1.00
CONTIG_MIN: 1
CONTIG_ID: 260
CONTIG_MAX: 1
S_END: 20937

Usage

... | assemble_contigs [options]

Options

[-?         | --help]               #  Print full usage description.
[-q         | --q_id]               #  Be Q_ID specific.
[-s         | --strand]             #  Be strand specific.
[-b         | --bridge]             #  Bridge mate-pair hits.
[-I <file!> | --stream_in=<file!>]  #  Read input from stream file  -  Default=STDIN
[-O <file>  | --stream_out=<file>]  #  Write output to stream file  -  Default=STDOUT
[-v         | --verbose]            #  Verbose output.

Examples

Author

Martin Asser Hansen - Copyright (C) - All rights reserved.

[email protected]

September 2009

License

GNU General Public License version 2

http://www.gnu.org/copyleft/gpl.html

Help

assemble_contigs is part of the Biopieces framework.

http://www.biopieces.org