Question

BWA.KIT where can i find it? Very confused

0

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5.4 years ago

Duarte Molha ▴ 240

Hi everyone

I am thinking if testing the bwa.post processing for alt contigs provided by bwa.kit... but I am very confused

BWA kit releases can be downloaded from here:

https://sourceforge.net/projects/bio-bwa/files/bwakit

and it seems it is hosted now on github here

https://github.com/lh3/bwa/tree/master/bwakit

but if you go to the github page , they say the contents of the package are : these:

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
|   |-- hs38DH-extra.fa        Decoy and HLA gene sequences. Used by run-gen-ref.
|   `-- hs38DH.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

I have downloaded the files and this content is no where to be found. All it contains is the source files to make bwa and a subfolder with the bwa.kit scripts for alt mapping, index building and post processing

What am I missing?

bwa bwakit alt_mapping • 3.8k views

ADD COMMENT • link updated 5.4 years ago by finswimmer 16k • written 5.4 years ago by Duarte Molha ▴ 240

score 1 · Accepted Answer · 2018-11-28

1

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5.4 years ago

finswimmer 16k

Hello Duarte Molha ,

where did you download? On github there are only the custom scripts by Heng Li hosted and not the additional binarys. The whole package is ready for download and contains all files you've listed above (and are mentioned on github).

fin swimmer

ADD COMMENT • link 5.4 years ago by finswimmer 16k

0

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unfortunately this is not the case ,, take a look at the folder called doc and the resource-human-HLA. and the other resource folder

none of those folders are on the downloads ... i know I checked

ADD REPLY • link 5.4 years ago by Duarte Molha ▴ 240

0

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I've downloaded bwakit-0.7.15_x64-linux.tar.bz2 from this source. After extracting the content of the bwa.kit folder looks like this:

$ tree .
.
├── README.md
├── bwa
├── bwa-postalt.js
├── doc
│   ├── NEWS.md
│   ├── README-alt.md
│   ├── README.md
│   └── bwa.1
├── fermi2
├── fermi2.pl
├── htsbox
├── k8
├── resource-GRCh38
│   ├── hs38DH-extra.fa
│   └── hs38DH.fa.alt
├── resource-human-HLA
│   ├── HLA-ALT-exons.bed
│   ├── HLA-ALT-idx
│   │   ├── alt_APD.fa.amb
│   │   ├── alt_APD.fa.ann
│   │   ├── alt_APD.fa.bwt
│   │   ├── alt_APD.fa.pac
│   │   ├── alt_APD.fa.sa
│   │   ├── alt_COX.fa.amb
│   │   ├── alt_COX.fa.ann
│   │   ├── alt_COX.fa.bwt
│   │   ├── alt_COX.fa.pac
│   │   ├── alt_COX.fa.sa
│   │   ├── alt_DBB.fa.amb
│   │   ├── alt_DBB.fa.ann
│   │   ├── alt_DBB.fa.bwt
│   │   ├── alt_DBB.fa.pac
│   │   ├── alt_DBB.fa.sa
│   │   ├── alt_MANN.fa.amb
│   │   ├── alt_MANN.fa.ann
│   │   ├── alt_MANN.fa.bwt
│   │   ├── alt_MANN.fa.pac
│   │   ├── alt_MANN.fa.sa
│   │   ├── alt_MCF.fa.amb
│   │   ├── alt_MCF.fa.ann
│   │   ├── alt_MCF.fa.bwt
│   │   ├── alt_MCF.fa.pac
│   │   ├── alt_MCF.fa.sa
│   │   ├── alt_QBL.fa.amb
│   │   ├── alt_QBL.fa.ann
│   │   ├── alt_QBL.fa.bwt
│   │   ├── alt_QBL.fa.pac
│   │   ├── alt_QBL.fa.sa
│   │   ├── alt_SSTO.fa.amb
│   │   ├── alt_SSTO.fa.ann
│   │   ├── alt_SSTO.fa.bwt
│   │   ├── alt_SSTO.fa.pac
│   │   ├── alt_SSTO.fa.sa
│   │   ├── pri_PGF.fa.amb
│   │   ├── pri_PGF.fa.ann
│   │   ├── pri_PGF.fa.bwt
│   │   ├── pri_PGF.fa.pac
│   │   └── pri_PGF.fa.sa
│   ├── HLA-ALT-type.txt
│   └── HLA-CDS.fa
├── ropebwt2
├── run-HLA
├── run-bwamem
├── run-gen-ref
├── samblaster
├── samtools
├── seqtk
├── trimadap
├── typeHLA-selctg.js
├── typeHLA.js
└── typeHLA.sh

Looks quite similar like the list on github.

ADD REPLY • link 5.4 years ago by finswimmer 16k

0

Entering edit mode

Ok ... I think I got what is wrong. I downloaded what I thought was the latest version from that link (0.7.17 file)

But the bwakit is the file below at version 0.7.15

Many thanks

Feeling a bit of an idiot :)

ADD REPLY • link 5.4 years ago by Duarte Molha ▴ 240