.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH FASTP "1" "April 2020" "fastp 0.20.1" "User Commands"
.SH NAME
fastp \- ultra-fast all-in-one FASTQ preprocessor
.SH DESCRIPTION
usage: ./fastp [options] ...
options:
.TP
\fB\-i\fR, \fB\-\-in1\fR
read1 input file name (string [=])
.TP
\fB\-o\fR, \fB\-\-out1\fR
read1 output file name (string [=])
.TP
\fB\-I\fR, \fB\-\-in2\fR
read2 input file name (string [=])
.TP
\fB\-O\fR, \fB\-\-out2\fR
read2 output file name (string [=])
.TP
\fB\-\-unpaired1\fR
for PE input, if read1 passed QC but read2 not, it will be written to unpaired1. Default is to discard it. (string [=])
.TP
\fB\-\-unpaired2\fR
for PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If \fB\-\-unpaired2\fR is same as \fB\-\-unpaired1\fR (default mode), both unpaired reads will be written to this same file. (string [=])
.TP
\fB\-\-failed_out\fR
specify the file to store reads that cannot pass the filters. (string [=])
.TP
\fB\-m\fR, \fB\-\-merge\fR
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 \fB\-\-merged_out\fR, the unmerged reads will be written to the files specified by \fB\-\-out1\fR and \fB\-\-out2\fR. The merging mode is disabled by default.
.TP
\fB\-\-merged_out\fR
in the merging mode, specify the file name to store merged output, or specify \fB\-\-stdout\fR to stream the merged output (string [=])
.TP
\fB\-\-include_unmerged\fR
in the merging mode, write the unmerged or unpaired reads to the file specified by \fB\-\-merge\fR. Disabled by default.
.TP
\fB\-6\fR, \fB\-\-phred64\fR
indicate the input is using phred64 scoring (it'll be converted to phred33, so the output will still be phred33)
.TP
\fB\-z\fR, \fB\-\-compression\fR
compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is 4. (int [=4])
.TP
\fB\-\-stdin\fR
input from STDIN. If the STDIN is interleaved paired\-end FASTQ, please also add \fB\-\-interleaved_in\fR.
.TP
\fB\-\-stdout\fR
stream passing\-filters reads to STDOUT. This option will result in interleaved FASTQ output for paired\-end output. Disabled by default.
.TP
\fB\-\-interleaved_in\fR
indicate that <in1> is an interleaved FASTQ which contains both read1 and read2. Disabled by default.
.TP
\fB\-\-reads_to_process\fR
specify how many reads/pairs to be processed. Default 0 means process all reads. (int [=0])
.TP
\fB\-\-dont_overwrite\fR
don't overwrite existing files. Overwritting is allowed by default.
.TP
\fB\-\-fix_mgi_id\fR
the MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it.
.TP
\fB\-V\fR, \fB\-\-verbose\fR
output verbose log information (i.e. when every 1M reads are processed).
.TP
\fB\-A\fR, \fB\-\-disable_adapter_trimming\fR
adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled
.TP
\fB\-a\fR, \fB\-\-adapter_sequence\fR
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])
.TP
\fB\-\-adapter_sequence_r2\fR
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])
.TP
\fB\-\-adapter_fasta\fR
specify a FASTA file to trim both read1 and read2 (if PE) by all the sequences in this FASTA file (string [=])
.TP
\fB\-\-detect_adapter_for_pe\fR
by default, the auto\-detection for adapter is for SE data input only, turn on this option to enable it for PE data.
.TP
\fB\-f\fR, \fB\-\-trim_front1\fR
trimming how many bases in front for read1, default is 0 (int [=0])
.TP
\fB\-t\fR, \fB\-\-trim_tail1\fR
trimming how many bases in tail for read1, default is 0 (int [=0])
.TP
\fB\-b\fR, \fB\-\-max_len1\fR
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])
.TP
\fB\-F\fR, \fB\-\-trim_front2\fR
trimming how many bases in front for read2. If it's not specified, it will follow read1's settings (int [=0])
.TP
\fB\-T\fR, \fB\-\-trim_tail2\fR
trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings (int [=0])
.TP
\fB\-B\fR, \fB\-\-max_len2\fR
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])
.TP
\fB\-g\fR, \fB\-\-trim_poly_g\fR
force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
.TP
\fB\-\-poly_g_min_len\fR
the minimum length to detect polyG in the read tail. 10 by default. (int [=10])
.TP
\fB\-G\fR, \fB\-\-disable_trim_poly_g\fR
disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
.TP
\fB\-x\fR, \fB\-\-trim_poly_x\fR
enable polyX trimming in 3' ends.
.TP
\fB\-\-poly_x_min_len\fR
the minimum length to detect polyX in the read tail. 10 by default. (int [=10])
.TP
\fB\-5\fR, \fB\-\-cut_front\fR
move a sliding window from front (5') to tail, drop the bases in the window if its mean quality < threshold, stop otherwise.
.TP
\fB\-3\fR, \fB\-\-cut_tail\fR
move a sliding window from tail (3') to front, drop the bases in the window if its mean quality < threshold, stop otherwise.
.TP
\fB\-r\fR, \fB\-\-cut_right\fR
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.
.TP
\fB\-W\fR, \fB\-\-cut_window_size\fR
the window size option shared by cut_front, cut_tail or cut_sliding. Range: 1~1000, default: 4 (int [=4])
.TP
\fB\-M\fR, \fB\-\-cut_mean_quality\fR
the mean quality requirement option shared by cut_front, cut_tail or cut_sliding. Range: 1~36 default: 20 (Q20) (int [=20])
.TP
\fB\-\-cut_front_window_size\fR
the window size option of cut_front, default to cut_window_size if not specified (int [=4])
.TP
\fB\-\-cut_front_mean_quality\fR
the mean quality requirement option for cut_front, default to cut_mean_quality if not specified (int [=20])
.TP
\fB\-\-cut_tail_window_size\fR
the window size option of cut_tail, default to cut_window_size if not specified (int [=4])
.TP
\fB\-\-cut_tail_mean_quality\fR
the mean quality requirement option for cut_tail, default to cut_mean_quality if not specified (int [=20])
.TP
\fB\-\-cut_right_window_size\fR
the window size option of cut_right, default to cut_window_size if not specified (int [=4])
.TP
\fB\-\-cut_right_mean_quality\fR
the mean quality requirement option for cut_right, default to cut_mean_quality if not specified (int [=20])
.TP
\fB\-Q\fR, \fB\-\-disable_quality_filtering\fR
quality filtering is enabled by default. If this option is specified, quality filtering is disabled
.TP
\fB\-q\fR, \fB\-\-qualified_quality_phred\fR
the quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified. (int [=15])
.TP
\fB\-u\fR, \fB\-\-unqualified_percent_limit\fR
how many percents of bases are allowed to be unqualified (0~100). Default 40 means 40% (int [=40])
.TP
\fB\-n\fR, \fB\-\-n_base_limit\fR
if one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5 (int [=5])
.TP
\fB\-e\fR, \fB\-\-average_qual\fR
if one read's average quality score <avg_qual, then this read/pair is discarded. Default 0 means no requirement (int [=0])
.TP
\fB\-L\fR, \fB\-\-disable_length_filtering\fR
length filtering is enabled by default. If this option is specified, length filtering is disabled
.TP
\fB\-l\fR, \fB\-\-length_required\fR
reads shorter than length_required will be discarded, default is 15. (int [=15])
.TP
\fB\-\-length_limit\fR
reads longer than length_limit will be discarded, default 0 means no limitation. (int [=0])
.TP
\fB\-y\fR, \fB\-\-low_complexity_filter\fR
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]).
.TP
\fB\-Y\fR, \fB\-\-complexity_threshold\fR
the threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required. (int [=30])
.TP
\fB\-\-filter_by_index1\fR
specify a file contains a list of barcodes of index1 to be filtered out, one barcode per line (string [=])
.TP
\fB\-\-filter_by_index2\fR
specify a file contains a list of barcodes of index2 to be filtered out, one barcode per line (string [=])
.TP
\fB\-\-filter_by_index_threshold\fR
the allowed difference of index barcode for index filtering, default 0 means completely identical. (int [=0])
.TP
\fB\-c\fR, \fB\-\-correction\fR
enable base correction in overlapped regions (only for PE data), default is disabled
.TP
\fB\-\-overlap_len_require\fR
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])
.TP
\fB\-\-overlap_diff_limit\fR
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])
.TP
\fB\-\-overlap_diff_percent_limit\fR
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])
.TP
\fB\-U\fR, \fB\-\-umi\fR
enable unique molecular identifier (UMI) preprocessing
.TP
\fB\-\-umi_loc\fR
specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none (string [=])
.TP
\fB\-\-umi_len\fR
if the UMI is in read1/read2, its length should be provided (int [=0])
.TP
\fB\-\-umi_prefix\fR
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 [=])
.TP
\fB\-\-umi_skip\fR
if the UMI is in read1/read2, fastp can skip several bases following UMI, default is 0 (int [=0])
.TP
\fB\-p\fR, \fB\-\-overrepresentation_analysis\fR
enable overrepresented sequence analysis.
.TP
\fB\-P\fR, \fB\-\-overrepresentation_sampling\fR
one in (\fB\-\-overrepresentation_sampling\fR) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20. (int [=20])
.TP
\fB\-j\fR, \fB\-\-json\fR
the json format report file name (string [=fastp.json])
.TP
\fB\-h\fR, \fB\-\-html\fR
the html format report file name (string [=fastp.html])
.TP
\fB\-R\fR, \fB\-\-report_title\fR
should be quoted with ' or ", default is "fastp report" (string [=fastp report])
.TP
\fB\-w\fR, \fB\-\-thread\fR
worker thread number, default is 2 (int [=2])
.TP
\fB\-s\fR, \fB\-\-split\fR
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])
.TP
\fB\-S\fR, \fB\-\-split_by_lines\fR
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])
.TP
\fB\-d\fR, \fB\-\-split_prefix_digits\fR
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])
.TP
\fB\-\-cut_by_quality5\fR
DEPRECATED, use \fB\-\-cut_front\fR instead.
.TP
\fB\-\-cut_by_quality3\fR
DEPRECATED, use \fB\-\-cut_tail\fR instead.
.TP
\fB\-\-cut_by_quality_aggressive\fR
DEPRECATED, use \fB\-\-cut_right\fR instead.
.TP
\fB\-\-discard_unmerged\fR
DEPRECATED, no effect now, see the introduction for merging.
.TP
\-?, \fB\-\-help\fR
print this message
.SH "SEE ALSO"
The full documentation for
.B fastp
is maintained as a Texinfo manual.  If the
.B info
and
.B fastp
programs are properly installed at your site, the command
.IP
.B info fastp
.PP
should give you access to the complete manual.