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add new command: --fastq_stats
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% vsearch-fastq_stats(1) version 2.30.0 | vsearch manual
% Torbjørn Rognes, Tomás Flouri, and Frédéric Mahé
#(./fragments/date.md)

# NAME

vsearch \-\-fastq_stats --- analyze fastq sequences and output
detailed statistics


# SYNOPSIS

| **vsearch** **\-\-fastq_stats** _fastqfile_ \-\-log _outputfile_ \[_options_]


# DESCRIPTION

The vsearch command `--fastq_stats` analyzes fastq sequences and
outputs detailed statistics, including projections of the impact
different filtering thresholds would have. Results are written to
`--log` *outputfile*. The quality encoding of the input fastq and the
range of accepted quality values can be specified with
`--fastq_ascii`, `--fastq_qmin` and `--fastq_qmax`.

The five different statistics tables reported by `--fastq_stats` are
described below, with an example for each.

## Read length distribution

Observed read lengths are sorted in decreasing order. The longest
length value is marked with '>='.

1. L: read length.
2. N: number of reads.
3. Pct: fraction of reads with this length.
4. AccPct: fraction of reads with this length or longer.

```text
Read length distribution
L N Pct AccPct
------- ---------- ------- -------
>= 251 19795 69.2% 69.2%
250 6847 23.9% 93.2%
249 1626 5.7% 98.9%
248 260 0.9% 99.8%
247 24 0.1% 99.8%
[...]
75 5 0.0% 100.0%
74 2 0.0% 100.0%
66 2 0.0% 100.0%
65 4 0.0% 100.0%
64 1 0.0% 100.0%
```


## Quality score distribution

Observed quality values are sorted in decreasing order.

1. ASCII: character encoding the quality score.
2. Q: Phred quality score.
3. Pe: probability of error associated with the quality score.
4. N: number of bases with this quality score.
5. Pct: fraction of bases with this quality score.
6. AccPct: fraction of bases with this quality score or higher.

```text
Q score distribution
ASCII Q Pe N Pct AccPct
----- --- ------- ---------- ------- -------
I 40 0.00010 2 0.0% 0.0%
H 39 0.00013 1009552 14.1% 14.1%
G 38 0.00016 1236861 17.3% 31.4%
F 37 0.00020 1231882 17.2% 48.6%
E 36 0.00025 330094 4.6% 53.2%
D 35 0.00032 143134 2.0% 55.2%
C 34 0.00040 250511 3.5% 58.7%
B 33 0.00050 451696 6.3% 65.0%
A 32 0.00063 273153 3.8% 68.8%
@ 31 0.00079 171356 2.4% 71.2%
? 30 0.00100 131957 1.8% 73.0%
> 29 0.00126 59308 0.8% 73.9%
= 28 0.00158 25174 0.4% 74.2%
< 27 0.00200 44282 0.6% 74.8%
; 26 0.00251 204896 2.9% 77.7%
: 25 0.00316 49600 0.7% 78.4%
9 24 0.00398 251427 3.5% 81.9%
6 21 0.00794 32 0.0% 81.9%
5 20 0.01000 11170 0.2% 82.0%
4 19 0.01259 9188 0.1% 82.2%
3 18 0.01585 34528 0.5% 82.7%
2 17 0.01995 25452 0.4% 83.0%
1 16 0.02512 100936 1.4% 84.4%
0 15 0.03162 96675 1.3% 85.8%
/ 14 0.03981 387620 5.4% 91.2%
. 13 0.05012 162798 2.3% 93.5%
- 12 0.06310 468864 6.5% 100.0%
```


## Length vs. quality distribution

Positions in reads are sorted in increasing order.

1. L: position in reads (starting from position 2).
2. PctRecs: fraction of reads with at least this length.
3. AvgQ: average quality score over all reads up to this position.
4. P(AvgQ): error probability corresponding to AvgQ.
5. AvgP: average error probability.
6. AvgEE: average expected error over all reads up to this position.
7. Rate: growth rate of AvgEE between this position and position - 1.
8. RatePct: Rate (as explained above) expressed as a percentage.

```text
L PctRecs AvgQ P(AvgQ) AvgP AvgEE Rate RatePct
----- ------- ---- ------- -------- ----- --------- --------
2 100.0% 28.2 0.00153 0.005655 0.01 0.005053 0.505%
3 100.0% 30.1 0.00097 0.002893 0.01 0.004333 0.433%
4 100.0% 27.7 0.00171 0.005935 0.02 0.004734 0.473%
5 100.0% 28.8 0.00131 0.004416 0.02 0.004670 0.467%
6 100.0% 29.5 0.00112 0.005633 0.03 0.004830 0.483%
[...]
247 99.8% 24.4 0.00360 0.019798 2.14 0.008668 0.867%
248 99.8% 24.0 0.00394 0.020644 2.16 0.008711 0.871%
249 98.9% 23.9 0.00407 0.020943 2.17 0.008716 0.872%
250 93.2% 23.8 0.00417 0.021239 2.22 0.008877 0.888%
251 69.2% 22.3 0.00589 0.023948 2.27 0.009048 0.905%
```


## Effect of expected error and length filtering

The first column indicates read lengths (L), sorted in decreasing
order, and starting with the first L with a cummulated expected error
smaller or equal to 1.0. The next four columns indicate the number of
reads that would be retained by the `--fastq_filter` command if the
reads were truncated at length L (option `--fastq_trunclen L`) and
filtered to have a maximum expected error of 1.0, 0.5, 0.25 or 0.1
(with the option `--fastq_maxee float`). The last four columns
indicate the fraction of reads that would be retained by the
`--fastq_filter` command using the same length and maximum expected
error parameters.

```text
L 1.0000 0.5000 0.2500 0.1000 1.0000 0.5000 0.2500 0.1000
----- ------- ------- ------- ------- ------- ------- ------- -------
251 6250 3022 1305 354 21.86% 10.57% 4.56% 1.24%
250 8894 4467 2080 637 31.10% 15.62% 7.27% 2.23%
249 9700 4930 2291 693 33.92% 17.24% 8.01% 2.42%
248 9854 5046 2348 712 34.46% 17.65% 8.21% 2.49%
247 9962 5127 2390 727 34.84% 17.93% 8.36% 2.54%
[...]
5 28595 28595 28595 28157 100.00% 100.00% 100.00% 98.47%
4 28595 28595 28595 28461 100.00% 100.00% 100.00% 99.53%
3 28595 28595 28595 28595 100.00% 100.00% 100.00% 100.00%
2 28595 28595 28595 28595 100.00% 100.00% 100.00% 100.00%
1 28595 28595 28595 28595 100.00% 100.00% 100.00% 100.00%
```


## Effect of minimum quality and length filtering

The first column indicates read lengths (Len), sorted in decreasing
order, and limited to the top *n* lengths, where n = floor(max length
/ 2) + 1. The next four columns indicate the fraction of reads that
would be retained by the `--fastq_filter` command if the reads were
truncated at length Len (option `--fastq_trunclen Len`) or at the
first position with a quality Q below 5, 10, 15 or 20 (option
`--fastq_truncqual Q`).

```text
Truncate at first Q
Len Q=5 Q=10 Q=15 Q=20
----- ------ ------ ------ ------
251 69.2% 69.2% 0.8% 0.6%
250 93.2% 93.2% 1.6% 1.1%
249 98.9% 98.9% 1.7% 1.2%
248 99.8% 99.8% 1.8% 1.2%
247 99.8% 99.8% 1.8% 1.2%
[...]
129 99.9% 99.9% 30.3% 10.3%
128 99.9% 99.9% 30.7% 10.4%
127 99.9% 99.9% 31.1% 10.5%
126 99.9% 99.9% 31.4% 10.5%
125 99.9% 99.9% 32.1% 10.7%
```


# OPTIONS

## mandatory options

#(./fragments/option_log.md)


## core options

#(./fragments/option_fastq_ascii.md)

#(./fragments/option_fastq_qmax.md)

#(./fragments/option_fastq_qmin.md)


## secondary options

#(./fragments/option_bzip2_decompress.md)

#(./fragments/option_gzip_decompress.md)

#(./fragments/option_no_progress.md)

#(./fragments/option_quiet.md)


## ignored options

#(./fragments/option_threads_not_multithreaded.md)


# EXAMPLES

Read from *input.fastq.gz*, do not write to the
standard error (`--quiet`), and write results to *output.log*
(`--log`):

```sh
vsearch \
--fastq_stats input.fastq.gz \
--quiet \
--log output.log
```

# SEE ALSO

[`vsearch-fastq_chars(1)`](./commands/vsearch-chars.1.md),
[`vsearch-fastq(5)`](../formats/vsearch-fastq.5.md)


#(./fragments/footer.md)

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