NAME
biox_map - a tool used to mapping and compare mapping result
VERSION
version 0.0.8
SYNOPSIS
biox_map command syntax:
biox_map <command> [options] [arguments]
Commands
map mapping one or more samples using bwa or soap
compare compare the result of bwa or soap
mapcompare a pipeline to mapping and compare result
See `biox_map --help` for the full documentation of biox_map, or
See `biox_map <command> --help` for detail description of the command
COMMAND: map
usage 1: using 2 cpu cores to map one file
biox_map map -i in.fastq -g hg19.fa -o out.txt -p 2
usage 2: batch mapping parallel, run 3 samples parallel with each one using 2 cpu
biox_map map -I indir -g hg19.fa -O outdir -p 2 -P 3
COMMAND: compare
useage: all mapping result stored in indir. suffix of soap result is '.soap'[default:.soap] and suffix of bwa result is '.sam'[default: .bwa].
biox_map compare -i indir -o summary.txt -s soap -b sam
COMMAND: mapcompare
useage: run 3 samples parallel with each one using 2 cpu, all result will be stored in outdir
biox_map mapcompare -i indir -o outdir -g hg.fa -s outdir/summary1.txt -p 2 -P 3
SEE ALSE
AUTHOR
Yan Xueqing <yanxueqing621@163.com>
COPYRIGHT AND LICENSE
This software is copyright (c) 2016 by Yan Xueqing.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.