Performs quality filtering and / or conversion of a
FASTQ file to FASTA format.
See also
Read quality filtering
FASTQ format options
Quality scores
Choosing FASTQ
filter parameters
Output options
| Option |
|
Description |
|
‑fastqout filename |
|
FASTQ
output file. You can use both ‑fastqout and ‑fastaout.
|
|
-fastaout filename |
|
FASTA
output file. You can use both ‑fastqout and ‑fastaout.
|
|
-relabel prefix |
|
Generate
new labels for the output sequences. They will be labeled prefix1,
prefix2 and so on. For example, if you use -prefix SampleA. then the labels
will be SampleA.1, SampleA.2 etc.
|
|
-eeout |
|
Append the
expected number of errors according to the Q
scores to the label in the format "ee=xx;". Expected errors are calculated after
truncation, if applicable.
|
Filtering options
| Option |
|
Description |
|
‑fastq_truncqual N |
|
Truncate
the read at the first position having quality score
<= N, so that all remaining Q scores are >N.
|
|
-fastq_maxee E |
|
Discard
reads with > E expected errors.
|
|
‑fastq_trunclen L |
|
Truncate
sequences at the L'th base. If the sequence is shorter than L, discard.
|
|
-fastq_minlen L |
|
Discard
sequences with < L letters.
|
Examples "Raw"
conversion of Sanger FASTQ to FASTA with no filtering:
usearch -fastq_filter reads.fastq -fastaout
reads.fasta -fastq_ascii 64 Truncate to length
150, discard if expected errors > 0.5, and convert to FASTA:
usearch -fastq_filter reads.fastq -fastq_trunclen
150 -fastq_maxee 0.5 \
-fastaout reads.fasta Truncate
a read at length 100 and then discard if it contains a Q<15, output to new FASTQ
file: usearch -fastq_filter reads.fastq -fastq_minlen
100 -fastq_truncqual 15 \
-fastqout filtered_reads.fastq
|