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. |
|
|
fastq_eestats fastq_eestats2 |
Report various statistics for FASTQ records. Useful for
understanding quality and
choosing FASTQ filter parameters. |