Provided by: fastp_0.20.0+dfsg-1_amd64 bug

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  --umpaired1  (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.

       -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.