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Fastest (non-pseudo) aligner for RNA-seq illumina seq data (year 2019)

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

rna-seq
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updated by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup • written by enxxx23 enxxx23

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

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written by WouterDeCoster WouterDeCoster 
for read in SeqIO.parse("reads.fastq.gz"):
    pass
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written by WouterDeCoster WouterDeCoster

They'd accept it, for sure.

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written by Kevin Blighe Kevin Blighe

At last try to :

read.seq == reference
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written by Bastien Hervé Bastien Hervé

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

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written by ddeemer • ddeemer

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.

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written by i.sudbery i.sudbery

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).

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written by GenoMax GenoMax

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

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written by enxxx23 enxxx23

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.

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written by GenoMax GenoMax

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! ;-)

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written by enxxx23 enxxx23

what do you mean by

Retroviruses do not have RNA

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written by Nicolas Rosewick Nicolas Rosewick

1 answer

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.

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written by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup

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

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written by WouterDeCoster WouterDeCoster

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