Question: Fastest (non-pseudo) aligner for RNA-seq illumina seq data (year 2019)
0
gravatar for enxxx23
23 months ago by
enxxx23240
European Union
enxxx23240 wrote:

What is the fastest (non-pseudo) aligner for RNA-seq illumina seq data today in year 2019?

rna-seq • 1.0k views
ADD COMMENTlink modified 23 months ago by kristoffer.vittingseerup3.5k • written 23 months ago by enxxx23240
1

fastest is a relative metric unless you do an apples-to-apples comparison on hardware you will eventually use. Choice of alignment options can have a significant impact on speed. It would be difficult to get those to align well among aligners.

bbmap.sh from BBMap suite will stand with the best of them on any given day.

bwa mem may be the smallest memory footprint aligner (~6-7G for human genome).

ADD REPLYlink modified 23 months ago • written 23 months ago by GenoMax95k

BWA MEM is not a RNA-seq aligner by design.

ADD REPLYlink written 23 months ago by enxxx23240

Sure. While the statement is true if you are looking for a splice-aware aligner it is not applicable in this case. Though you could use it if you were dealing with bacterial RNAseq data.

ADD REPLYlink modified 23 months ago • written 23 months ago by GenoMax95k

True, I should have mentioned the target organisms, which in this case are eukaryotes. Retroviruses do not have RNA so doing RNA-seq on retroviruses is the only choice! ;-)

ADD REPLYlink written 22 months ago by enxxx23240

what do you mean by

Retroviruses do not have RNA

ADD REPLYlink modified 22 months ago • written 22 months ago by Nicolas Rosewick9.3k

I don't believe that speed only is a valuable concept. I could write an EXTREMELY fast aligner (with terrible accuracy).

ADD REPLYlink written 23 months ago by WouterDeCoster45k
1

Challenge accepted !

ADD REPLYlink written 23 months ago by Nicolas Rosewick9.3k
3
for read in SeqIO.parse("reads.fastq.gz"):
    pass
ADD REPLYlink written 23 months ago by WouterDeCoster45k

ok great. Now submit to Nature Methods

ADD REPLYlink written 23 months ago by Nicolas Rosewick9.3k

They'd accept it, for sure.

ADD REPLYlink written 23 months ago by Kevin Blighe69k

At last try to :

read.seq == reference
ADD REPLYlink written 23 months ago by Bastien Hervé4.9k

if read in reference: print('Aligned!')

ADD REPLYlink written 22 months ago by ddeemer10

STAR is for me, the best compromise between running time and efficiency

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5792058/

ADD REPLYlink written 23 months ago by Bastien Hervé4.9k
1

I think STAR and HiSAT are probably similar. STAR requires less tuning, but HiSAT can be tuned to give very similar accuracy performance. The benefit of HiSAT is that it uses much less memory.

ADD REPLYlink written 23 months ago by i.sudbery10k
1
gravatar for kristoffer.vittingseerup
23 months ago by
European Union
kristoffer.vittingseerup3.5k wrote:

The better choices are:

  1. Salmon
  2. Kallisto

Both are very fast and highly accurate. Unless you have large differences in GC content there is no better tool - then they perform very similar. If you have a high GC-content Salmon is probably the better option due to its gcBias algorithm.

ADD COMMENTlink written 23 months ago by kristoffer.vittingseerup3.5k

OP explicitly mentioned being looking for aligners, not pseudo-aligners...

ADD REPLYlink written 23 months ago by WouterDeCoster45k

Woops - Missed the -non :D

ADD REPLYlink written 23 months ago by kristoffer.vittingseerup3.5k
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