bwa
Burrows-Wheeler Alignment tool.
TLDR
Index the reference genome
$ bwa index [path/to/reference.fa]
Map single-end reads (sequences) to indexed genome using 32 [t]hreads and compress the result to save space
$ bwa mem -t 32 [path/to/reference.fa] [path/to/read_single_end.fq.gz] | gzip > [path/to/alignment_single_end.sam.gz]
Map pair-end reads (sequences) to the indexed genome using 32 [t]hreads and compress the result to save space
$ bwa mem -t 32 [path/to/reference.fa] [path/to/read_pair_end_1.fq.gz] [path/to/read_pair_end_2.fq.gz] | gzip > [path/to/alignment_pair_end.sam.gz]
Map pair-end reads (sequences) to the indexed genome using 32 [t]hreads with [M]arking shorter split hits as secondary for output SAM file compatibility in Picard software and compress the result
$ bwa mem -M -t 32 [path/to/reference.fa] [path/to/read_pair_end_1.fq.gz] [path/to/read_pair_end_2.fq.gz] | gzip > [path/to/alignment_pair_end.sam.gz]
Map pair-end reads (sequences) to indexed genome using 32 [t]hreads with FASTA/Q [C]omments (e.g. BC:Z:CGTAC) appending to a compressed result
$ bwa mem -C -t 32 [path/to/reference.fa] [path/to/read_pair_end_1.fq.gz] [path/to/read_pair_end_2.fq.gz] | gzip > [path/to/alignment_pair_end.sam.gz]
