---
name: "fastp"
section: "1"
platform: "linux"
package: "fastp"
version: "0.24.0+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastp"
---

# fastp(1)

Ultra-fast all-in-one FASTQ preprocessor

## NAME

fastp - Ultra-fast all-in-one FASTQ preprocessor

## DESCRIPTION

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

## AUTHOR

 This manpage was written by Nilesh Patra for the Debian distribution and\
  can be used for any other usage of the program.