is there any comparation of Cloud based aligner?? SEAL, Crossbow etc

[asleo]

Hello~ nice to meet you~~

I'm using Hadoop system for resequencing NGS DATA.

i have used Crossbow for align but some NGS data is not fit to crossbow

becasue bowtie used in crossbow does not consider gap.

Becasuse of that reason, i'm trying to use other program like

SEAL which use bwa or other hadoop base programs using bowtie2.


Can anyone recommand me a good application for me??

[kopi-o]

I'm not sure what your question is exactly, but Seal is the only open Hadoop-based tool I know of where you can align with gaps (because it uses bwa as you say). Why not try it?

[wanguan2000]

hello, when i run the example of crossbow i got this problem:

Crossbow expects 'bowtie' to be at path /home/wanguan2000/hadoop_soft/crossbow-1.2.0/bin/bowtie on the workers
Crossbow expects 'soapsnp' to be at path /home/wanguan2000/hadoop_soft/crossbow-1.2.0/bin/soapsnp on the workers
Crossbow expects 'fastq-dump' to be at path /home/wanguan2000/hadoop_soft/sratoolkit.2.1.16-centos_linux64/bin/fastq-dump on the workers
But in all my hadoop computers have those program in the same path.
And I used the test command to test all computers.
$CROSSBOW_HOME/cb_hadoop --test

Checking $PATH...
Found '/home/wanguan2000/hadoop_soft/sratoolkit.2.1.16-centos_linux64/bin/fastq-dump'...
Runnable?....YES
Summary:
bowtie: INSTALLED at /home/wanguan2000/hadoop_soft/crossbow-1.2.0/bin/bowtie
soapsnp: INSTALLED at /home/wanguan2000/hadoop_soft/crossbow-1.2.0/bin/soapsnp
Hadoop note: executables must be runnable via the SAME PATH on all nodes.
PASSED install test

It seems all ok in my all hadoop computers.
Anyone can help me.
BTW: Does crossbow remove or ignore PCR duplicate reads in SNP calling