Foss Equivalent To Clc Assembly Cell?

Question

[Science_Robot]

CLC Assembly Cell is both fast and sensitive. Is there a FOSS alternative?

(Specifically, I am aligning short reads to NCBI NR gene sequences to get coverage)

So far, I have tried Bowtie, BLAST, Maq and Mosaik but nothing comes close.

EDIT:

The data is 2x100bp Illumina shotgun metagenome data. I use NR, SEED and all bacterial genomes as my databases.

[Sean Davis]

From what organism are your reads? What type of reads Illumina, 454, solid? What read length and are the reads paired? This is RNA-seq? And why use NCBI NR?

Answer 1

[lh3]

[?]Firstly, you may want to change your pipeline. There are more sophisticated approaches for computing coverage using RNA-seq data.[?]

As to your question, the CLC mapper does local alignment (if I am right), while most of the mainstream NGS mappers do glocal alignment. Based on this difference, you can exclude bowtie, maq, soap1/2/3, bwa, gsnap, novoalign, rmap and many others. BLAST is similar to the CLC mapper, but I guess it is too slow.

A few fast mappers do local alignment like the CLC mapper. You may consider bwa-sw and smalt. BFAST may be a viable option, too. I do not know for sure.

[?]In the end, to increase the chance of getting a better answer, you should provide more details about what you are doing. You should also explain why the aligners you mention are "nothing comes close".[?]

EDIT: for your application, you may try bwa-sw and smalt. If the default configuration fails, you may consider to change the parameter to make them more sensitive (for bwa-sw, increase -z to -z10 or so).

[Aaronquinlan]

@lh3: have you done any direct comparisons b/w bwa-sw and smalt for split alignments?

[lh3]

Have not done for smalt, but from what I heard, smalt is similar to ssaha2 in many aspects, just much faster.

[lh3]

Have not done for smalt, but from what I heard, smalt is similar to ssaha2 in many aspects, just much faster. It is also designed for doing chimeric alignment, while many tools not.

[Science_Robot]

@lh3 I've never heard of smalt. It looks like it might suit my needs (mincoverage and minidentity). Thanks.