FASTP(1)

✨ NAME ✨

fastp — Ultra-fast all-in-one FASTQ preprocessor. (Yes bestie, this is FASTP(1), User Commands, and she's that girl. 💅)

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🦋 DESCRIPTION 🦋

okay so fastp is an ultra-fast all-in-one FASTQ preprocessor, version 0.23.0, and the usage is literally:

fastp [options] ...

options:

bestie, defaults are doing main character energy here — read them before you override, fr fr.

• -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]) ✨

okay that's all the options in part 1 — part 2 is coming, don't go anywhere bestie 💖

• --umi_prefix — bestie, if you set this, an underline is gonna glue your prefix and your UMI together like they're holding hands 🫶 so like prefix=UMI, UMI=AATTCG, and boom, the final result is UMI_AATTCG. No prefix by default. (string [=])
• --umi_skip — if your UMI is chillin' in read1/read2, fastp can skip a few bases right after the UMI, no questions asked. Default is 0, so it skips nothing unless you tell it to. (int [=0])
• -p, --overrepresentation_analysis — turns on overrepresented sequence analysis. Basically fastp goes 👀 at sequences that show up way too much.
• -P, --overrepresentation_sampling — one in (--overrepresentation_sampling) reads gets computed for the overrepresentation analysis, and the valid range is 1~10000. Smaller number = slower, bc obviously you're checking more reads. Default is 20. (int [=20])
• -j, --json — the name for your json format report file. (string [=fastp.json])
• -h, --html — the name for your html format report file. (string [=fastp.html])
• -R, --report_title — the title of your report, and ngl you have to quote it with ' or " or it'll be mad at you. Default is "fastp report". (string [=fastp report])
• -w, --thread — how many worker threads you want doing the actual work. Default is 3. (int [=3])
• -s, --split — splits your output by capping the total number of split files with this option (2~999). A sequential number prefix gets added to the output name, so you get stuff like 0001.out.fq, 0002.out.fq, and so on. It's disabled by default, so nothing splits unless you ask. (int [=0])
• -S, --split_by_lines — splits your output by capping the number of lines per file with this option (>=1000). Same deal, a sequential number prefix gets added to the output name (0001.out.fq, 0002.out.fq...). Disabled by default. (long [=0])
• -d, --split_prefix_digits — how many digits go into padding that sequential number, valid range is 1~10, default is 4, so your filenames get padded like 0001.xxx. Set it to 0 to disable padding entirely. (int [=4])
• --cut_by_quality5 — DEPRECATED, use --cut_front instead. She's retired, okay? 💅
• --cut_by_quality3 — DEPRECATED, use --cut_tail instead. Also retired, move on bestie.
• --cut_by_quality_aggressive — DEPRECATED, use --cut_right instead. Yeah she's gone too.
• --discard_unmerged — DEPRECATED and it does literally nothing now, no cap. See the introduction for merging. It's giving ghost of options past 👻
• -?, --help — prints this message. That's it, that's the whole job. 🎀

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💖 AUTHOR 💖

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. Shoutout to him, fr fr 🙌

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And that's the whole page, bestie!! This was fastp 0.23.0, dated October 2021, living in section FASTP(1) of your manual. Go read your reads and slay ✨💅🦋