SNP Detection

[Oxygen81]

Hello everybody,

I am searching for some software with which it is possible to align 454 contigs against a reference sequence and to detect SNPs. It is essential that the quality file is considered and that a table with Position, SNP and quality is written in the output. Has anyone an idea?

Thank you in advance
Janina

[nickloman]

Try gsMapper (part of Newbler) supplied by Roche.

[krobison]

The software wiki lists a number of packages specifically in this space (454 SNP Discovery); you might also look at the other Snp Discovery packages as many are platform agnostic.

[SoftGenetics]

Hello everybody,

I am searching for some software with which it is possible to align 454 contigs against a reference sequence and to detect SNPs. It is essential that the quality file is considered and that a table with Position, SNP and quality is written in the output. Has anyone an idea?

Thank you in advance
Janina

NextGENe will do a great and easy job on this, also has a quality ranking, like Phred, for all found variants including indels

[geschickten]

Hi Janina, do you have gsMapper or any other similar s/w? if not write to me; I can probably help you...

[Oxygen81]

Hello,

thank you all for your fast answers! I already tried CLC genomic workbench and Genious which are great but they don't display the quality of the detected SNPs. Maybe I have to make clear that I don't mean the quality of the SNP but of the sequenced base (for 454: 0-64). I asked our sequencing facility about the use of the gsMapper but they told me that it is not possible to import assembled contigs and no quality files, too... Is that right?
I will try NextGENe if there is a trial version available. Thank you all!

[Nomijill]

Display of confidence scores

You should be able to view the quality scores of all of your bases in the Genomics Workbench. It is a display option. If you want, I can show you how.

[link1]

agreed gsmapper

[Dethecor]

Why gsmapper?

Hi all,

just a question that popped into my mind. (I normally use output from Illumina machines)

Why do you need to use this gsmapper tool instead of a standard SNP-calling pipeline like:

sequencer -> read-file -> [bwa|bowtie|...(aligner of your choice)] -> output.sam-file

and then just run 'samtools pileup' on your output file and get the SNP's with quality and all from there?

I was just wondering if there is something special about 454-reads, that renders this approach unfeasible?

Cheers,
Paul

[sklages]

agreed gsmapper

gsMapper will align 454 reads and will refuse mapping sequences longer than a certain threshold, like contigs.

[sklages]

Hi all,

just a question that popped into my mind. (I normally use output from Illumina machines)

Why do you need to use this gsmapper tool instead of a standard SNP-calling pipeline like:

sequencer -> read-file -> [bwa|bowtie|...(aligner of your choice)] -> output.sam-file

and then just run 'samtools pileup' on your output file and get the SNP's with quality and all from there?

I was just wondering if there is something special about 454-reads, that renders this approach unfeasible?

Cheers,
Paul

454 reads are longer and are not fixed-length; the short read aligners are not the approbiate tools for that kind of sequencing data.

And, he was asking to map contigs, not reads. Although, I would map the reads and look for variations .. :-)

[SoftGenetics]

You may wish to test the aligner in NextGENe which also provides a high level of visualization and annotation.

[DNASTAR]

Hi Janina,

Lasergene's SeqMan app can assemble 454 data against a reference, and detect SNPs. The SNP reports will display the imported quality scores, position, SNP base, as well as a lot of other useful info. You can learn more or get a free trial here.

Thanks,
Anne