Illumina HiSeq library insert size - Page 2

fanli · 03-08-2017, 08:49 AM

You might find this benchmark to be helpful:
http://www.nature.com/articles/srep19233

My understanding is that you are better off using newer k-mer based approaches as opposed to BLAST. I've had reasonable success with kraken, although the memory requirements are somewhat onerous. You also have to be extremely careful about removing contaminant (aka human) sequences as these tend to get misclassified.

Another option is kallisto (https://github.com/pachterlab/metakallisto) but I have yet to be able to even build a database due to memory constraints.

SDPA_Pet · 03-08-2017, 08:51 AM

Quote:

Originally Posted by fanli

You might find this benchmark to be helpful:
http://www.nature.com/articles/srep19233

My understanding is that you are better off using newer k-mer based approaches as opposed to BLAST. I've had reasonable success with kraken, although the memory requirements are somewhat onerous. You also have to be extremely careful about removing contaminant (aka human) sequences as these tend to get misclassified.

Another option is kallisto (https://github.com/pachterlab/metakallisto) but I have yet to be able to even build a database due to memory constraints.

I will try. Can you gimme the Kraken link? Thanks.

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03-08-2017, 08:49 AM	#21
fanli Senior Member Location: California Join Date: Jul 2014 Posts: 198	You might find this benchmark to be helpful: http://www.nature.com/articles/srep19233 My understanding is that you are better off using newer k-mer based approaches as opposed to BLAST. I've had reasonable success with kraken, although the memory requirements are somewhat onerous. You also have to be extremely careful about removing contaminant (aka human) sequences as these tend to get misclassified. Another option is kallisto (https://github.com/pachterlab/metakallisto) but I have yet to be able to even build a database due to memory constraints.