Question: sequence alignment vs mapping
0
gravatar for andynkili
4.8 years ago by
andynkili10
andynkili10 wrote:

i would like to identify a set of reads (that i will later assemble regarding their taxonomic affiliations), and i've tested sequence alignment (BLAST) and read mapping (Bowtie2). The thing is, i'm not sure which one i should trust for my read classification.

ADD COMMENTlink modified 4.8 years ago by glihm620 • written 4.8 years ago by andynkili10

Could you precise a little bit please. Which kind of reads? 16S? RNA-seq?

ADD REPLYlink written 4.8 years ago by glihm620

reads are coming from whole genome sequencing. Samples come from human subjects and then are sequenced on Illumina Miseq.

ADD REPLYlink written 4.8 years ago by andynkili10
2
gravatar for Devon Ryan
4.8 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

Well, blast is a bit more sensitive than bowtie2, however bowtie2 is vastly faster than blast. So, what to choose is based more on how much data you have to go through and how many computers you can throw at the problem (unless time isn't an issue, in which case enjoy just using blast).

BTW, both blast and bowtie2 produce alignments (in addition to mapping sequences).

ADD COMMENTlink written 4.8 years ago by Devon Ryan95k
2
gravatar for glihm
4.8 years ago by
glihm620
France
glihm620 wrote:

I agree with the Devon's answer. An other thing to take in account is which kind or read you have, pair-ended and long reads, or short reads for example.

You have here a benchmark (2015) about NGS short read mappers, it may helps you to determine which one you can use, and what are the differences between these tools. 

I hope this helps you! ;)

 

ADD COMMENTlink written 4.8 years ago by glihm620

thanks for the benchmark!

ADD REPLYlink written 4.8 years ago by andynkili10
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