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FASTQ commands

Most search and clustering commands support FASTQ files as input. USEARCH automatically detects whether the file is in FASTQ format (first byte is @) or FASTQ format (first byte is >).

See also
FASTQ files
  Quality scores
  Expected errors
  Average Q is a bad idea!
  FASTQ format options
Wikipedia article on FASTQ
  Cock et al (2010) paper describing FASTQ
  Choosing FASTQ filter parameters

Command   Description
fastq_chars   Report frequency and range of ASCII characters used to represent quality scores. Useful for guessing the FASTQ score parameters of a file.
fastq_filter   Quality filtering and / or conversion of FASTQ to FASTA format. See also choosing FASTQ filter parameters.
fastq_mergepairs   Merge paired reads into single reads. Sometimes also called overlapping or (perhaps misleadingly) assembly of paired reads.
fastq_stats   Report various statistics for FASTQ records. Useful for choosing FASTQ filter parameters.
fastq_join   Combine paired reads into single sequences by inserting padding (NNNNNNNN). Useful for paired reads that are separated by a gap, so do not overlap.
  Report various statistics for FASTQ records. Useful for understanding quality and choosing FASTQ filter parameters.