Report statistics on reads in a
FASTQ file. Useful for choosing FASTQ
See also the
fastq_eestats command, which has more and better reports.
Output is written to a file specified by the
-log filename command-line option.
FASTQ format options
are supported, these must be specified if the Q scores are specified using
non-default ASCII characters.
reads.fastq -log stats.log
The log file format is subject to change. It is meant to be human-readable
rather than parsed by a script. It would be nice to have an option to write the
information to a format like tabbed text that can easily be parsed or imported
into a program such as Excel that can make charts. Hopefully I will add this
feature in the near future; please
let me know
if you need this.
This section reports the read length distribution. Columns are: L=read
length, N=number of reads, Pct=fraction of reads with this length, AccPct=fraction
of reads that are greater than or equal to this length.
Q score distribution
This section reports the number of bases found for each Q score. Columns
are: ASCII=symbol, Q=integer Phred score,
N=number of bases, Pct=number of bases with this Q score, AccPct=number of bases
with >= this Q score.
Length vs. quality distribution
This section shows the fraction of records and average
expected number of errors obtained by
truncating at each possible position in the read. Columns are: L=position in
read, PctRecs=fraction of reads with at least this length, AvgQ=average Q score
over all reads obtained by truncating at this position, P(AvgQ)=error
probability corresponding to AvgQ, AvgP=average error probability
Expected error truncation summary
This section summarizes the effect of some common choices of max. expected
errors trunction (fastq_filter command with -fastq_maxee
and -fastq_trunclen options). L=truncation length, columns 1.0, 0.5, 0.25 and
0.1 give the number of reads and the fraction of reads respectively that would
pass a filter with the options given (-fastq_trunclen=L and -fastq_maxee=1.0,
0.5, 0.25 or 0.1).
Minimum Q truncation summary
This section summarizes the effect of length truncation with some common
choices of minimum Q (fastq_filter command with
‑fastq_trunclen options). Len is the truncation
length (‑fastq_trunclen option), the other columns
give the fraction of reads that pass that filter.