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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.



fastq_join command

See also
FASTQ files
  Quality scores
  FASTQ format options

The fastq_join command combines paired reads into single sequences by reverse-complementing the reverse read and inserting padding (default NNNNNNNN). If R1 is the forward read and R2 is the reversed read, the combined read is R1 NNNNNNNN RevComp(R2).

The forward (R1) read filename is given by the fastq_join option.

The reverse (R2) read filename is given by the -reverse option.

The -join_padgap option specifies the letters to use for padding, default NNNNNNNN.

The -join_padgapq option specifies the Q score ASCII characters to use for padding, default IIIIIIII (8 x Q=40 with ASCII_BASE 33).

The output is written to a FASTQ file by specifying the -fastqout option and/or to a FASTA file given by -fastaout.


usearch -fastq_join fwd.fastq -reverse rev.fastq -fastaout join.fa