build the bwa index

perform the bwa alignment

snakemake wrapper for single or paired end alignment

single-end alignment

Align using mem algorithm. To use BWA, you need to first index the genome with `bwa index'. There are three alignment algorithms in BWA `mem', `bwasw', and `aln/samse/sampe'. If you are not sure which use, try `bwa mem' first.

index sequences in the FASTA format

paired end alignment