Bwakit is a self-consistent installation-free package of scripts and precompiled
binaries which provide an end-to-end solution to read mapping. In addition to
the basic mapping functionality implemented in bwa, bwakit is able to generate
proper human reference genome and to take advantage of ALT contigs, if present,
to improve read mapping and to perform HLA typing for high-coverage human data.
It can remap name- or coordinate-sorted BAM with read group and barcode
information retained. Bwakit also *optionally* trims adapters (via
[trimadap][ta]), marks duplicates (via [samblaster][sb]) and sorts the final
alignment (via [samtools][smtl]).

Bwakit has two entry scripts: `run-gen-ref` which downloads and generates human
reference genomes, and `run-bwamem` which prints mapping command lines on the
standard output that can be piped to `sh` to execute. The two scripts will call
other programs or use data in `bwa.kit`. The following shows an example about
how to use bwakit:

```sh
# Download the bwa-0.7.11 binary package (download link may change)
wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.11_x64-linux.tar.bz2/download \
  | gzip -dc | tar xf -
# Generate the GRCh38+ALT+decoy+HLA and create the BWA index
bwa.kit/run-gen-ref hs38d6   # download GRCh38 and write hs38d6.fa
bwa.kit/bwa index hs38d6.fa  # create BWA index
# mapping
bwa.kit/run-bwamem -o out hs38d6.fa read1.fq read2.fq | sh
```

The last mapping command line will generate the following files:

* `out.aln.bam`: unsorted alignments with ALT-aware mapping quality. In this
  file, one read may be placed on multiple overlapping ALT contigs at the same
  time even if the read is mapped better to some contigs than others. This makes
  it possible to analyze each contig independent of others.

* `out.hla.top`: best genotypes for HLA-A, -B, -C, -DQA1, -DQB1 and -DRB1 genes.

* `out.hla.all`: other possible genotypes on the six HLA genes.

* `out.log.*`: bwa-mem, samblaster and HLA typing log files.

Bwakit can be [downloaded here][res]. It is only available to x86_64-linux. The
scripts in the package are available in the [bwa/bwakit][kit] directory.
Packaging is done manually for now.


[res]: https://sourceforge.net/projects/bio-bwa/files/
[sb]: https://github.com/GregoryFaust/samblaster
[ta]: https://github.com/lh3/seqtk/blob/master/trimadap.c
[smtl]: http://www.htslib.org
[kit]: https://github.com/lh3/bwa/tree/master/bwakit