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+Program: bwa (alignment via Burrows-Wheeler transformation)
+Version: 0.7.17-r1188
+Contact: Heng Li <lh3@sanger.ac.uk>
+
+Usage:   bwa <command> [options]
+
+Command: index         index sequences in the FASTA format
+         mem           BWA-MEM algorithm
+         fastmap       identify super-maximal exact matches
+         pemerge       merge overlapping paired ends (EXPERIMENTAL)
+         aln           gapped/ungapped alignment
+         samse         generate alignment (single ended)
+         sampe         generate alignment (paired ended)
+         bwasw         BWA-SW for long queries
+
+         shm           manage indices in shared memory
+         fa2pac        convert FASTA to PAC format
+         pac2bwt       generate BWT from PAC
+         pac2bwtgen    alternative algorithm for generating BWT
+         bwtupdate     update .bwt to the new format
+         bwt2sa        generate SA from BWT and Occ
+
+Note: 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 to use, try `bwa mem'
+      first. Please `man ./bwa.1' for the manual.