What is a robust short read to wgs reference aligner?
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6.7 years ago
vassialk ▴ 200

What is a robust short read to wgs reference aligner? Need a tool to perform alignment of 180 .sra and .fastaq files to tuberculosis .gb reference genome. Have tried NextGene. Need a free alternative. Tried Ugene, CLC, DnaStar, GenPro. All are resource demanding and slow.

soft wgs sequencing • 1.6k views
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6.7 years ago

BBMap is free and very robust. bwa-mem is also free, and typically faster, but less sensitive. SNAP is also free, and even faster than BBMap or bwa-mem, but even less sensitive. Generally, there is a tradeoff between speed and sensitivity when you do alignment, so the choice of aligner depends on your goals.

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I don't know much about them, and have never tested them. Are you talking about Sailfish?

BBDuk, though, can sort of do pseudo-alignment. Specifically, it can count how many bases in a read are covered by kmers that match a reference (mincoveredfraction) flag, which should be more precise than simply counting the number of kmers shared with a reference. I have not compared the sensitivity or specificity to mapping or to simply counting kmers.

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I am also referring to Kallisto...