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

BioX::Map

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.