https://github.com/xerial/genome-weaver-align

Toolkit for genome sciences
https://github.com/xerial/genome-weaver-align

Last synced: 9 months ago
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Toolkit for genome sciences

• Host: GitHub
• URL: https://github.com/xerial/genome-weaver-align
• Owner: xerial
• Created: 2012-05-30T02:39:20.000Z (over 13 years ago)
• Default Branch: develop
• Last Pushed: 2012-08-23T08:15:10.000Z (over 13 years ago)
• Last Synced: 2025-04-13T00:58:53.370Z (9 months ago)
• Language: Java
• Homepage: http://xerial.org/genome-weaver
• Size: 3.62 MB
• Stars: 3
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          

# Genome Weaver - A Toolkit for Genome Sciences

* align - FM-index based Aligner

* lens	- Data format reader (FASTA,FASTQ,BED,WIG,GFF,SAM/BAM,etc.)

## Install

```

$ make install

```

Default installation folder is ```$HOME/local/bin/genome-weaver```

### Building BWT index 

```

$ JVM_OPT="-Xmx=32g" genome-weaver bwt hg19.fa 

```

### Single-end alignment

```

$ genome-weaver align -r hg19.fa (fastq file)  > (sam file)

```

### Paired-end alignment

 (soon)

 

### Configure your Git

```

$ git confgi core.eol lf

$ git config core.autocrlf input

```