325 B

Raw Blame History

FastAlign

Fast alignment tool based on bwa-mem

1. Compile the source code

make -j 8

2. Build the FMT-Index

./fastalign index reference.fasta

3. Run sequence alignment with FastAlign

./fastalign mem -t 64 -2 -M -R @RG\tID:normal\tSM:normal\tPL:illumina\tLB:normal\tPG:fastbwa reference.fasta r1.fq.gz r2.fq.gz