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bwa_seq
Martin Asser Hansen edited this page Oct 2, 2015
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bwa_seq uses BWA to map sequences in the stream against a specified index created with format_genome. Sequences can originate from Solexa or FASTQ type entries only (no FASTA). bwa_seq.
The resulting records are based on the SAM format (http://samtools.sourceforge.net/) and look like this:
MAPQ: 37
FLAG: 0
SCORES: a```aa_a]aa^^`a]a`]`_`_]^a_S[_\R^]^YUYU[[[X^
Q_ID: 1_pZnOjxwXsN1
S_ID: M1_c29
REC_TYPE: SAM
S_BEG2: 6062
S_BEG: 6060
ISIZE: 0
SEQ: TATCAGCGTATGTCGTTACGTTACCGGCATGTGTATTCACTGTT
CIGAR: 44M
MRNM: =
---
BWA must be installed for bwa_seq to work. Read more about BWA here:
... | bwa_seq [options] -g <genome>
or
... | bwa_seq [options] -i <index>
[-? | --help] # Print full usage description.
[-g <genome!> | --genome=<genome!>] # Choose target genome (instead of index).
[-i <string> | --index_name=<string>] # Choose target index (instead of genome).
[-h <uint> | --max_hits=<uint>] # Max hits to report - Default=all
[-c <uint> | --cpus=<uint>] # Number of CPUs to use - Default=1
[-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.
In order to use bwa_seq to map a stack of query sequences from a FASTQ file to a specified index previously created with create_bwa_index, do:
read_fastq -i query_sequences.fq | bwa_seq -i ~/my_dir/myindex
Martin Asser Hansen - Copyright (C) - All rights reserved.
September 2009
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
bwa_seq is part of the Biopieces framework.