What is a robust short read to wgs reference aligner?
1
0
Entering edit mode
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
ADD COMMENT
0
Entering edit mode
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.

ADD COMMENT
0
Entering edit mode
Bryan.. And what is your opinion about the new pseudo aligners?
ADD REPLY
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode
I am also referring to Kallisto...
ADD REPLY

Login before adding your answer.

Traffic: 794 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6