.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.5.
.TH FASTP "1" "October 2021" "fastp 0.23.0" "User Commands"
.SH NAME
fastp \- Ultra-fast all-in-one FASTQ preprocessor
.SH DESCRIPTION
fastp: an ultra\-fast all\-in\-one FASTQ preprocessor
version 0.23.0
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\-\-overlapped_out\fR
for each read pair, output the overlapped region if it has no any mismatched base. (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\-D\fR, \fB\-\-dedup\fR
enable deduplication to drop the duplicated reads/pairs
.TP
\fB\-\-dup_calc_accuracy\fR
accuracy level to calculate duplication (1~6), higher level uses more memory (1G, 2G, 4G, 8G, 16G, 24G). Default 1 for no\-dedup mode, and 3 for dedup mode. (int [=0])
.TP
\fB\-\-dont_eval_duplication\fR
don't evaluate duplication rate to save time and use less memory.
.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 3 (int [=3])
.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 AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.