Question: Open Source Sequence Assembly Programs
4
gravatar for Monzoor
8.3 years ago by
Monzoor290
Monzoor290 wrote:

Can anyone suggest a simple open source light weight assembly tool which i can use on a simple desktop for assembling max of 20000 to 30000 sequences.

Note: I have myself simulated these sequences from 10 genomes. The idea was to create an artificial metagenomics data set). Consequently I do not have quality files for these sequences. Please do not suggest me to use FAMES data set, as I have already benchmarked my experiment using these data sets.

ADD COMMENTlink modified 8.3 years ago by Bach550 • written 8.3 years ago by Monzoor290
5
gravatar for Spitshine
8.3 years ago by
Spitshine640
Esch-sur-Alzette, Luxembourg
Spitshine640 wrote:

CAP3 and PCAP (http://seq.cs.iastate.edu/) by Xiaoqiu Huang (http://www.cs.iastate.edu/~xqhuang/) are easy to use. We've been using CAP3 for assembly of simulated data for teaching.

ADD COMMENTlink written 8.3 years ago by Spitshine640
4
gravatar for Bach
8.3 years ago by
Bach550
Bach550 wrote:

Shameless plug: MIRA3 at SourceForge with the the corresponding Wiki where you can find the full manual online. It is one self-contained binary, ready to run if you download the binary package.

Input formats can be any of the usual suspects (FASTA, FASTQ, PHD, EXP), giving ancillary data is also possible (NCBI TRACEINFO XML, EXP, tab delimited files).

You might be interested in using the feature where you can assign strain data to your reads and have the assembler mark SNPs and other differences when assembling all reads together. This works both for mapping as well as for de-novo assemblies. See some examples here.

You can also tell the assembler which sequencing technologiy your (in this case simulated) sequences are and see how it influences assembly and SNP calling (e.g., indels will not be called SNPs in 454 sequences by default, but in Sanger and Illumina sequences they will).

On a last note: as you have no qualities, you will need to tell the assembler about it. See here for information on how to do that.

ADD COMMENTlink written 8.3 years ago by Bach550
3
gravatar for Stephan
8.3 years ago by
Stephan150
europe
Stephan150 wrote:

I know a online tool, can take a couple of hours. And don't know your fileformat but have a look: http://egassembler.hgc.jp/

http://www.phrap.org/phredphrapconsed.html

http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS

ADD COMMENTlink written 8.3 years ago by Stephan150
2
gravatar for Rm
8.3 years ago by
Rm7.8k
Danville, PA
Rm7.8k wrote:

IDBA de-novo assembly

ADD COMMENTlink written 8.3 years ago by Rm7.8k

Thanks Raghu. The tool looks interesting. I will try it out and let you know.

ADD REPLYlink written 8.3 years ago by Monzoor290
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1801 users visited in the last hour