what is the detailed information of .amb .ann .bwt .pac .sa files generated by the BWA aligner?

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6.2 years ago

lffu_0032 ▴ 90

i am new to bwa aligner, and i indexed hg19 chr1 using BWA [index] method: bwa index -p hg19.chr1 -a bwtsw /Users/lffu/bio-info/reference/genome/hg19/chr1.fa

after running this command, it generated 5 files: hg19.chr1.amb hg19.chr1.ann hg19.chr1.bwt hg19.chr1.pac hg19.chr1.sa

i looked through the bwa official web page and its tutorial, but i did not find more information about the detail meaning of these files, so can anyone help me explain the exact meaning of these 5 files? many thanks here.

alignment BWA .ann .bwt .sa • 8.9k views

ADD COMMENT • link updated 6.2 years ago by WouterDeCoster 47k • written 6.2 years ago by lffu_0032 ▴ 90

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They're internal files needed by BWA, their exact meaning and contents are otherwise irrelevant.

ADD REPLY • link 6.2 years ago by Devon Ryan 104k

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These files represent the burrows-wheeler transformed genome as well as the respective suffix array etc. As Devon said, irrelevant for the end user. If you want details, refer to the BWA paper.