Provided by: fastp_0.20.1+dfsg-1_amd64 
NAME
fastp - ultra-fast all-in-one FASTQ preprocessor
DESCRIPTION
usage: ./fastp [options] ... options:
-i, --in1
read1 input file name (string [=])
-o, --out1
read1 output file name (string [=])
-I, --in2
read2 input file name (string [=])
-O, --out2
read2 output file name (string [=])
--unpaired1
for PE input, if read1 passed QC but read2 not, it will be written to unpaired1.
Default is to discard it. (string [=])
--unpaired2
for PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If
--unpaired2 is same as --unpaired1 (default mode), both unpaired reads will be
written to this same file. (string [=])
--failed_out
specify the file to store reads that cannot pass the filters. (string [=])
-m, --merge
for paired-end input, merge each pair of reads into a single read if they are
overlapped. The merged reads will be written to the file given by --merged_out, the
unmerged reads will be written to the files specified by --out1 and --out2. The
merging mode is disabled by default.
--merged_out
in the merging mode, specify the file name to store merged output, or specify
--stdout to stream the merged output (string [=])
--include_unmerged
in the merging mode, write the unmerged or unpaired reads to the file specified by
--merge. Disabled by default.
-6, --phred64
indicate the input is using phred64 scoring (it'll be converted to phred33, so the
output will still be phred33)
-z, --compression
compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is
4. (int [=4])
--stdin
input from STDIN. If the STDIN is interleaved paired-end FASTQ, please also add
--interleaved_in.
--stdout
stream passing-filters reads to STDOUT. This option will result in interleaved
FASTQ output for paired-end output. Disabled by default.
--interleaved_in
indicate that <in1> is an interleaved FASTQ which contains both read1 and read2.
Disabled by default.
--reads_to_process
specify how many reads/pairs to be processed. Default 0 means process all reads.
(int [=0])
--dont_overwrite
don't overwrite existing files. Overwritting is allowed by default.
--fix_mgi_id
the MGI FASTQ ID format is not compatible with many BAM operation tools, enable
this option to fix it.
-V, --verbose
output verbose log information (i.e. when every 1M reads are processed).
-A, --disable_adapter_trimming
adapter trimming is enabled by default. If this option is specified, adapter
trimming is disabled
-a, --adapter_sequence
the adapter for read1. For SE data, if not specified, the adapter will be
auto-detected. For PE data, this is used if R1/R2 are found not overlapped. (string
[=auto])
--adapter_sequence_r2
the adapter for read2 (PE data only). This is used if R1/R2 are found not
overlapped. If not specified, it will be the same as <adapter_sequence> (string
[=auto])
--adapter_fasta
specify a FASTA file to trim both read1 and read2 (if PE) by all the sequences in
this FASTA file (string [=])
--detect_adapter_for_pe
by default, the auto-detection for adapter is for SE data input only, turn on this
option to enable it for PE data.
-f, --trim_front1
trimming how many bases in front for read1, default is 0 (int [=0])
-t, --trim_tail1
trimming how many bases in tail for read1, default is 0 (int [=0])
-b, --max_len1
if read1 is longer than max_len1, then trim read1 at its tail to make it as long as
max_len1. Default 0 means no limitation (int [=0])
-F, --trim_front2
trimming how many bases in front for read2. If it's not specified, it will follow
read1's settings (int [=0])
-T, --trim_tail2
trimming how many bases in tail for read2. If it's not specified, it will follow
read1's settings (int [=0])
-B, --max_len2
if read2 is longer than max_len2, then trim read2 at its tail to make it as long as
max_len2. Default 0 means no limitation. If it's not specified, it will follow
read1's settings (int [=0])
-g, --trim_poly_g
force polyG tail trimming, by default trimming is automatically enabled for
Illumina NextSeq/NovaSeq data
--poly_g_min_len
the minimum length to detect polyG in the read tail. 10 by default. (int [=10])
-G, --disable_trim_poly_g
disable polyG tail trimming, by default trimming is automatically enabled for
Illumina NextSeq/NovaSeq data
-x, --trim_poly_x
enable polyX trimming in 3' ends.
--poly_x_min_len
the minimum length to detect polyX in the read tail. 10 by default. (int [=10])
-5, --cut_front
move a sliding window from front (5') to tail, drop the bases in the window if its
mean quality < threshold, stop otherwise.
-3, --cut_tail
move a sliding window from tail (3') to front, drop the bases in the window if its
mean quality < threshold, stop otherwise.
-r, --cut_right
move a sliding window from front to tail, if meet one window with mean quality <
threshold, drop the bases in the window and the right part, and then stop.
-W, --cut_window_size
the window size option shared by cut_front, cut_tail or cut_sliding. Range: 1~1000,
default: 4 (int [=4])
-M, --cut_mean_quality
the mean quality requirement option shared by cut_front, cut_tail or cut_sliding.
Range: 1~36 default: 20 (Q20) (int [=20])
--cut_front_window_size
the window size option of cut_front, default to cut_window_size if not specified
(int [=4])
--cut_front_mean_quality
the mean quality requirement option for cut_front, default to cut_mean_quality if
not specified (int [=20])
--cut_tail_window_size
the window size option of cut_tail, default to cut_window_size if not specified
(int [=4])
--cut_tail_mean_quality
the mean quality requirement option for cut_tail, default to cut_mean_quality if
not specified (int [=20])
--cut_right_window_size
the window size option of cut_right, default to cut_window_size if not specified
(int [=4])
--cut_right_mean_quality
the mean quality requirement option for cut_right, default to cut_mean_quality if
not specified (int [=20])
-Q, --disable_quality_filtering
quality filtering is enabled by default. If this option is specified, quality
filtering is disabled
-q, --qualified_quality_phred
the quality value that a base is qualified. Default 15 means phred quality >=Q15 is
qualified. (int [=15])
-u, --unqualified_percent_limit
how many percents of bases are allowed to be unqualified (0~100). Default 40 means
40% (int [=40])
-n, --n_base_limit
if one read's number of N base is >n_base_limit, then this read/pair is discarded.
Default is 5 (int [=5])
-e, --average_qual
if one read's average quality score <avg_qual, then this read/pair is discarded.
Default 0 means no requirement (int [=0])
-L, --disable_length_filtering
length filtering is enabled by default. If this option is specified, length
filtering is disabled
-l, --length_required
reads shorter than length_required will be discarded, default is 15. (int [=15])
--length_limit
reads longer than length_limit will be discarded, default 0 means no limitation.
(int [=0])
-y, --low_complexity_filter
enable low complexity filter. The complexity is defined as the percentage of base
that is different from its next base (base[i] != base[i+1]).
-Y, --complexity_threshold
the threshold for low complexity filter (0~100). Default is 30, which means 30%
complexity is required. (int [=30])
--filter_by_index1
specify a file contains a list of barcodes of index1 to be filtered out, one
barcode per line (string [=])
--filter_by_index2
specify a file contains a list of barcodes of index2 to be filtered out, one
barcode per line (string [=])
--filter_by_index_threshold
the allowed difference of index barcode for index filtering, default 0 means
completely identical. (int [=0])
-c, --correction
enable base correction in overlapped regions (only for PE data), default is
disabled
--overlap_len_require
the minimum length to detect overlapped region of PE reads. This will affect
overlap analysis based PE merge, adapter trimming and correction. 30 by default.
(int [=30])
--overlap_diff_limit
the maximum number of mismatched bases to detect overlapped region of PE reads.
This will affect overlap analysis based PE merge, adapter trimming and correction.
5 by default. (int [=5])
--overlap_diff_percent_limit
the maximum percentage of mismatched bases to detect overlapped region of PE reads.
This will affect overlap analysis based PE merge, adapter trimming and correction.
Default 20 means 20%. (int [=20])
-U, --umi
enable unique molecular identifier (UMI) preprocessing
--umi_loc
specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read,
default is none (string [=])
--umi_len
if the UMI is in read1/read2, its length should be provided (int [=0])
--umi_prefix
if specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI,
UMI=AATTCG, final=UMI_AATTCG). No prefix by default (string [=])
--umi_skip
if the UMI is in read1/read2, fastp can skip several bases following UMI, default
is 0 (int [=0])
-p, --overrepresentation_analysis
enable overrepresented sequence analysis.
-P, --overrepresentation_sampling
one in (--overrepresentation_sampling) reads will be computed for
overrepresentation analysis (1~10000), smaller is slower, default is 20. (int
[=20])
-j, --json
the json format report file name (string [=fastp.json])
-h, --html
the html format report file name (string [=fastp.html])
-R, --report_title
should be quoted with ' or ", default is "fastp report" (string [=fastp report])
-w, --thread
worker thread number, default is 2 (int [=2])
-s, --split
split output by limiting total split file number with this option (2~999), a
sequential number prefix will be added to output name ( 0001.out.fq,
0002.out.fq...), disabled by default (int [=0])
-S, --split_by_lines
split output by limiting lines of each file with this option(>=1000), a sequential
number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled
by default (long [=0])
-d, --split_prefix_digits
the digits for the sequential number padding (1~10), default is 4, so the filename
will be padded as 0001.xxx, 0 to disable padding (int [=4])
--cut_by_quality5
DEPRECATED, use --cut_front instead.
--cut_by_quality3
DEPRECATED, use --cut_tail instead.
--cut_by_quality_aggressive
DEPRECATED, use --cut_right instead.
--discard_unmerged
DEPRECATED, no effect now, see the introduction for merging.
-?, --help
print this message
SEE ALSO
The full documentation for fastp is maintained as a Texinfo manual. If the info and fastp
programs are properly installed at your site, the command
info fastp
should give you access to the complete manual.