Hi All,
I need to run some analyses on large datasets that I will be analysing in MEGAN. I need to run BLASTX and BLASTN (like) searches, but both programs are very very slow and I constantly run into programs with not allocating enough memory. Does anybody know of other programs I could use instead of BLAST? I have been looking into the following:
LAST
USEARCH
FR-HIT
RapSearch
Overall I think they should all be faster than blast, but they also come with various problems - some of them don't output blast-format and others don't control memory very well (e.g. I need to blast against the nr database with 2gigs of ram). Any ideas or suggestions? I'm leaning towards LAST as I can control memory quite well, but I'm not sure how fast it is and it also doesn't directly output to blast format.
I welcome any suggestions - thanks.
I need to run some analyses on large datasets that I will be analysing in MEGAN. I need to run BLASTX and BLASTN (like) searches, but both programs are very very slow and I constantly run into programs with not allocating enough memory. Does anybody know of other programs I could use instead of BLAST? I have been looking into the following:
LAST
USEARCH
FR-HIT
RapSearch
Overall I think they should all be faster than blast, but they also come with various problems - some of them don't output blast-format and others don't control memory very well (e.g. I need to blast against the nr database with 2gigs of ram). Any ideas or suggestions? I'm leaning towards LAST as I can control memory quite well, but I'm not sure how fast it is and it also doesn't directly output to blast format.
I welcome any suggestions - thanks.
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