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Greetings, just curious if anyone out there has used to CD-HIT-454 to cluster Illumina data, rather than 454 data, and about how long it them to get back a collapsed result. I'm trying to "decompress" the number of unique reads before starting a large blastx run against a 16S rRNA gene database, and then NCBI-nr. I' started running the CD-HIT-454 on Friday afternoon, and its still running. The command I used is below:
$nohup cd-hit-454 -i N5_bioCollapsed.fasta -o N5_bio_c90.fasta -c 0.9 -n 5 -M 2000
My input file (N5_bioCollapsed.fasta) has 3884222 100bp reads. This sequence data was produced through sequencing of DNA recovered from an agricultural soil. My end goal is to assess the frequency of functional genes in the sample to other samples collected from similar sites, under differing conditions.
If anyone else has complimentary methods they have found useful for dereliction/redundancy filtering, please let me know. Thanks,
-tony
$nohup cd-hit-454 -i N5_bioCollapsed.fasta -o N5_bio_c90.fasta -c 0.9 -n 5 -M 2000
My input file (N5_bioCollapsed.fasta) has 3884222 100bp reads. This sequence data was produced through sequencing of DNA recovered from an agricultural soil. My end goal is to assess the frequency of functional genes in the sample to other samples collected from similar sites, under differing conditions.
If anyone else has complimentary methods they have found useful for dereliction/redundancy filtering, please let me know. Thanks,
-tony