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.
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Science_Robot
[?]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).
@lh3: have you done any direct comparisons b/w bwa-sw and smalt for split alignments?
@lh3 I've never heard of smalt. It looks like it might suit my needs (mincoverage and minidentity). Thanks.
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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?