moved directory structure to this README

There are too many README files...
seankhl · Nov 19, 2014 · 6609baf · 6609baf
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commit 6609baf
Showing 1 changed file with 43 additions and 0 deletions.
diff --git a/bwakit/README.md b/bwakit/README.md
@@ -1,3 +1,5 @@
+## Introduction
+
 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
 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.
 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
 [sb]: https://github.com/GregoryFaust/samblaster