Comments for MassGenomics

Comment on Short Read Aligners: Maq, Eland, and Others by Sparks

Sparks — Thu, 31 Jul 2008 06:54:05 +0000

Hi all,
I’ve just put an update to novoalign & novopaired. This update improves quality scores for novopaired and also fixes a illegal instruction fault reported by one user.
You can download at http://www.novocraft.com
I’ve also changed the license term so it’s free for any non-profit even if you don’t publish in open journals.
Colin

Comment on Helicos Resequences M13 Virus Genome by PolITiGenomics » Blog Archive » In the dark

PolITiGenomics » Blog Archive » In the dark — Tue, 15 Jul 2008 15:25:02 +0000

[...] my colleague posted a write-up of the recent Helicos publication in Science on their sequencing of the M13 virus genome. [...]

Comment on Short Read Aligners: Maq, Eland, and Others by zayedi

zayedi — Wed, 09 Jul 2008 03:45:32 +0000

A new short-read aligner, novoalign, has just been released. It’s free for academic/non-profit use and works pretty well with Illumina reads.

Some features are:

* Gaps up to 7bp, affine gap penalties
* Can handle ambiguous codes in ref sequence.
* Quality-based scoring
* Adapter stripping for miRNA reads
* No heuristics – reports the best alignment
* Options for handling multiple alignments includes none, random, all alignments.
* Alignment Quality scores
* Can use fasta, fastq, solexa fastq, prb input formats
* Paired end with full Needleman-Wunsch on both ends.
* Paired end accepts a structural variation penalty and the best alignment may be two independent ends if score with SV penalty is better than the best pair that fits the fragment length distribution.
* Supports variable read lengths
* Includes optional soft masking of repeats.
* Iterative read trimming

Give it a whirl. In terms of performance it’s quite fast, some users have commented that it runs faster than the SOAP program.

Have a read on the website http://www.novocraft.com and download the executables for 64-bit Linux and Mac OS 10.5.3.

Comment on Short Read Aligners: Maq, Eland, and Others by jhui

jhui — Thu, 19 Jun 2008 20:19:50 +0000

SeqMap (http://biogibbs.stanford.edu/~jiangh/SeqMap/) – work like ELand, can do 3 or more bp mismatches and also insdel

Comment on Short Read Aligners: Maq, Eland, and Others by Subcutaneous

Subcutaneous — Thu, 19 Jun 2008 04:07:29 +0000

Somehow i missed the point. Probably lost in translation Anyway … nice blog to visit.

cheers, Subcutaneous.

Comment on Short Read Aligners: Maq, Eland, and Others by zayedi

zayedi — Tue, 17 Jun 2008 09:29:41 +0000

I’m still not so keen on using eland in situations when my reads are less than 25bp but greater than 20bp e.g with microRNAs sequenced from Solexa. The FP question can only reliably answered on testing various scenarios where we actually know where our reads will map.
Something I’ve also seen is that you may not align a read where there are ambiguous characters around the mid-section of the short sequence read.
Using paired-end will definitely push up FP but with higher read errors, indels, etc, the curve for PE alignment may look better.

Comment on Short Read Aligners: Maq, Eland, and Others by John Castle

John Castle — Thu, 12 Jun 2008 00:07:10 +0000

Has anyone tested Biostrings (in Bioconductor) or qpalma(http://www.fml.tuebingen.mpg.de/raetsch/projects/qpalma/qpalma-final.pdf) [uses Vmatch]?

Comment on About by Deanne Taylor

Deanne Taylor — Fri, 23 May 2008 17:44:09 +0000

Thanks for all the great posts! I think our interests overlap.

Comment on Short Read Aligners: Maq, Eland, and Others by Sparks

Sparks — Thu, 22 May 2008 07:05:59 +0000

To:ac
I can think of two drawbacks on using Eland as a preprocess to maq.
First is that you won’t pick up any short indels with Eland, only SNPs so if you remove NM reads you might miss any short indel polymorphisms.
Second is that Eland can align with max of 2 mismatches where maq can handle more. Again only problem if you remove NM reads.
You could consider retaining NM reads for input to maq.

Comment on Short Read Aligners: Maq, Eland, and Others by ac

ac — Mon, 19 May 2008 15:36:09 +0000

“The main contributor (other is read quality) to FPs is repeats or near repeats so a read has alternative alignment locations. Sometimes this will result in one alignment which may turn out to be a FP. Sometimes we’ll get multiple alignments with the same score. With MAQ, its habit of randomly choosing one alignment from a set of equal scoring alignments introduces some FP and some extra (random) TP. Other tools just report the read as having multiple alignments which some evaluations report as a FN.”

We generally get around this by providing only uniquely aligned reads from Eland as input to MAQ. The obvious drawback to this is that you may be losing some reads. However, I haven’t seen any drop in depth beyond 1X unless it is a highly repetitive region. Fortunately we did see some FPs go away with this approach but does anyone see any drawbacks?