evaluate novoalign

[GoogleCodeExporter]

download novoalign
install

try on bis data

Original issue reported on code.google.com by zack...@gmail.com on 4 May 2012 at 6:26

[GoogleCodeExporter]

installed novoalign, 

created wrapper

tested on 200K line fastq

modified existing bisulfite worlflow to optionally support novoalign.

usage: 
#bsmap
Sample.7.Workflow = bisulfite

#novoalign
Sample.7.Workflow = bisulfite-novo

currently testing on flowcell C0D, from my shorter test, novoalign is quite 
slow...

Original comment by zack...@gmail.com on 15 May 2012 at 12:13

[GoogleCodeExporter]

yaping was in contact with the guys from novoalign and the following cmd lines 
is being tested:

$novo -d $refNovo -f $read1 $read2 -F ILMFQ -b 2 -o SAM -k -t 240 -l 50  > 
$outfileSAM

Original comment by zack...@gmail.com on 21 May 2012 at 7:06

[GoogleCodeExporter]

lung tumor / lung normal, all lanes are being reprocessed with novoalign. 

Original comment by zack...@gmail.com on 21 May 2012 at 9:28

[GoogleCodeExporter]

I've created a walker to compare the differences between novo and bsmap

running on lung tumor

Original comment by zack...@gmail.com on 5 Jun 2012 at 8:02

• Changed title: evaluate novoalign

[GoogleCodeExporter]

closing this redundant ticket in favor of later, more detailed tickets 
regarding novoalign

Original comment by zack...@gmail.com on 30 Jul 2012 at 8:29

• Changed state: Duplicate