assemble_contigs
Martin Asser Hansen edited this page Oct 2, 2015
·
6 revisions
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
... | assemble_contigs [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.
Martin Asser Hansen - Copyright (C) - All rights reserved.
September 2009
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
assemble_contigs is part of the Biopieces framework.