fastp - Ultra-fast all-in-one FASTQ preprocessor
fastp: an ultra-fast all-in-one FASTQ preprocessor version 0.23.0
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
[=])
- --overlapped_out
- for each read pair, output the overlapped region if it has no any
mismatched base. (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])
- -D, --dedup
- enable deduplication to drop the duplicated reads/pairs
- --dup_calc_accuracy
- 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])
- --dont_eval_duplication
- don't evaluate duplication rate to save time and use less memory.
- -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 3 (int [=3])
- -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
This manpage was written by Nilesh Patra for the Debian
distribution and
can be used for any other usage of the program.