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BWA Version 1
BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.
Input Parameters
Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]
Help information

Version 1
Usage: -a -e -f -in1 -in2 -l -k -n -o
-a      mem/aln/pemerge
-e      single_end/paired_end
-f      reference file
-in1    fastq1
-in2    fastq2
-l      INT     seed length [32]
-k      INT     maximum differences in the seed [2]
-n      NUM     max #diff (int) or missing prob under 0.02 err rate (float) [0.04]
-o      output_file_name

Parameters Description
-a: Algorithms in BWA
alignment algorithms in BWA: mem/aln/pemerge
-e: Expriment Method
Expriment Method of Sequencing: single_end/paired_end
-f: Reference
-in1: Fastq file upload
Fastq file upload
-in2: Fastq file upload
Fastq file upload
-l: Seed Length
Seed Length
-k: Maximum differences in the seed
maximum differences in the seed
-n: Max #diff (int) or missing prob under 0.02 err rate (float)
Max #diff (int) or missing prob under 0.02 err rate (float)