Reference
Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]
Help information
BWA2
Version 1
Usage:
bwa.pl -a -e -f -in1 -in2 -l -k -n -o
opts:
-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 |
| 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) |
