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moved directory structure to this README 

There are too many README files...
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Heng Li 2014-11-19 12:45:21 -05:00
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bwakit/README.md
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## Introduction
Bwakit is a self-consistent installation-free package of scripts and precompiled Bwakit is a self-consistent installation-free package of scripts and precompiled
binaries, providing an end-to-end solution to read mapping. In addition to the binaries, providing an end-to-end solution to read mapping. In addition to the
basic mapping functionality implemented in bwa, bwakit is able to generate basic mapping functionality implemented in bwa, bwakit is able to generate
@ -42,6 +44,47 @@ 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. scripts in the package are available in the [bwa/bwakit][kit] directory.
Packaging is done manually for now. Packaging is done manually for now.
## Contents
```
bwa.kit
|-- README.md This README file.
|-- run-bwamem *Entry script* for the entire mapping pipeline.
|-- bwa *BWA binary*
|-- k8 Interpretor for *.js scripts.
|-- bwa-postalt.js Post-process alignments to ALT contigs/decoys/HLA genes.
|-- htsbox Used by run-bwamem for shuffling BAMs and BAM=>FASTQ.
|-- samblaster MarkDuplicates for reads from the same library. v0.1.20
|-- samtools SAMtools for sorting and SAM=>BAM conversion. v1.1
|-- seqtk For FASTQ manipulation.
|-- trimadap Trim Illumina PE sequencing adapters.
|
|-- run-gen-ref *Entry script* for generating human reference genomes.
|-- resource-GRCh38 Resources for generating GRCh38
| |-- hs38d6-decoy.nt.anno Top decoy-to-nt hits. Not used by any scripts.
| |-- hs38d6-decoy.rm.out RepeatMasker report. Not used.
| |-- hs38d6-extra.fa Decoy and HLA gene sequences. Used by run-gen-ref.
| `-- hs38d6.fa.alt ALT-to-GRCh38 alignment. Used by run-gen-ref.
|
|-- run-HLA HLA typing for sequences extracted by bwa-postalt.js.
|-- typeHLA.sh Type one HLA-gene. Called by run-HLA.
|-- typeHLA.js HLA typing from exon-to-contig alignment. Used by typeHLA.sh.
|-- typeHLA-selctg.js Select contigs overlapping HLA exons. Used by typeHLA.sh.
|-- fermi2.pl Fermi2 wrapper. Used by typeHLA.sh for de novo assembly.
|-- fermi2 Fermi2 binary. Used by fermi2.pl.
|-- ropebwt2 RopeBWT2 binary. Used by fermi2.pl.
|-- resource-human-HLA Resources for HLA typing
| |-- HLA-ALT-exons.bed Exonic regions of HLA ALT contigs. Used by typeHLA.sh.
| |-- HLA-CDS.fa CDS of HLA-{A,B,C,DQA1,DQB1,DRB1} genes from IMGT/HLA-3.18.0.
| |-- HLA-ALT-type.txt HLA types for each HLA ALT contig. Not used.
| `-- HLA-ALT-idx BWA indices of each HLA ALT contig. Used by typeHLA.sh
| `-- (...)
|
`-- doc BWA documentations
|-- bwa.1 Manpage
|-- NEWS.md Release Notes
|-- README.md GitHub README page
`-- README-alt.md Documentation for ALT mapping
```
[res]: https://sourceforge.net/projects/bio-bwa/files/bwakit [res]: https://sourceforge.net/projects/bio-bwa/files/bwakit
[sb]: https://github.com/GregoryFaust/samblaster [sb]: https://github.com/GregoryFaust/samblaster