Overview

= 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)