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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



fastx_getsubseq command

See also


Extract a subsequence from a FASTA or FASTQ file. The label is given by the -label option. The start-end coordinates are specified by the subseq_start and subseq_end options.

Positions, are 1-based so are in the range 1, 2 ... L where L is the sequence length.

Both -subseq_start and/or -subseq_end may be omitted, they default to 1 and L respectively.

If the -label_substr_match option is specified, then the label given on the command-line may be a substring of a sequence label.

Output is written to -fastaout (FASTA) and/or -fastqout (FASTQ). You cannot use -fastqout if the input is FASTA because the quality scores are not known.


usearch -fastx_getsubseq human.fa -label chr7 -subseq_start 1677654 -subseq_end 1677699 \
  -fastaout chr7_segment.fa