looking for reference genome based assembler for short-reads

zchou · 12-16-2009, 11:27 AM

Hi All,

I want to use comparative-based assembler for short-reads for assembling mRNA-seq. For example, if we have human tissue mRNA short-reads, we want to reassemble the short-reads into transcripts by comparing with human genome, which software is more suitable for this task?

I found AMOScmp-shortreads might be useful for this purpose, but when I read the manual, I found AMOScmp do not support fastq format. I also don't know the performance for this software.

In further, do anyone compare the performance of de novo based assembler with reference-based assembler for mRNA-seq?

Thanks,
ZCH

krobison · 12-16-2009, 06:51 PM

The RNA-Seq section of the software wiki at this site has 14 entries; not all of them perform mapping but you should find several tools there which might be candidates for your needs.

http://seqanswers.com/wiki/Special:B...domain=RNA-Seq

zchou · 12-16-2009, 08:26 PM

As the lists of this webpage "Software packages for next gen sequence analysis" includes many different tools for mapping/assembling. However, no any software designed for this purpose. MAQ has limited function to generate the consensus sequences based on mapping. However, it seems MAQ can only use reads length lower than 63bp. As I listed, AMOScmp-short-reads is only software I know to provide this function, but weak support for paired-end illumina GAII sequences files(qseq) or fastq.

Xi Wang · 12-16-2009, 09:13 PM

Check Tophat and Cufflink.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Genome Res De novo bacterial genome sequencing: millions of very short reads assembly	b_seite	Literature Watch	1	10-05-2017 12:26 AM
Ray: a NEW MPI-based 100% parallel genome assembler	seb567	Bioinformatics	278	12-10-2015 06:25 AM
hg19 genome reference for short read mapping	yh253	Bioinformatics	4	12-29-2013 10:11 PM
Looking for assembler to align very short reads	andylai	Bioinformatics	0	06-02-2011 09:58 PM
Short reads fragments of genome...	hicham	Bioinformatics	2	03-24-2010 05:15 AM

12-16-2009, 11:27 AM	#1
zchou Member Location: detroit, US Join Date: May 2009 Posts: 13	looking for reference genome based assembler for short-reads Hi All, I want to use comparative-based assembler for short-reads for assembling mRNA-seq. For example, if we have human tissue mRNA short-reads, we want to reassemble the short-reads into transcripts by comparing with human genome, which software is more suitable for this task? I found AMOScmp-shortreads might be useful for this purpose, but when I read the manual, I found AMOScmp do not support fastq format. I also don't know the performance for this software. In further, do anyone compare the performance of de novo based assembler with reference-based assembler for mRNA-seq? Thanks, ZCH

12-16-2009, 09:13 PM	#4
Xi Wang Senior Member Location: MDC, Berlin, Germany Join Date: Oct 2009 Posts: 317	Check Tophat and Cufflink. __________________ Xi Wang

12-16-2009, 06:51 PM	#2
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	The RNA-Seq section of the software wiki at this site has 14 entries; not all of them perform mapping but you should find several tools there which might be candidates for your needs. http://seqanswers.com/wiki/Special:B...domain=RNA-Seq

12-16-2009, 08:26 PM	#3
zchou Member Location: detroit, US Join Date: May 2009 Posts: 13	As the lists of this webpage "Software packages for next gen sequence analysis" includes many different tools for mapping/assembling. However, no any software designed for this purpose. MAQ has limited function to generate the consensus sequences based on mapping. However, it seems MAQ can only use reads length lower than 63bp. As I listed, AMOScmp-short-reads is only software I know to provide this function, but weak support for paired-end illumina GAII sequences files(qseq) or fastq.