PORECHOP(1)

✨ PORECHOP ✨

okay bestie, welcome to porechop — the manual page, but make it a group chat 💅 this is a tool for finding adapters in Oxford Nanopore reads, trimming them off the ends and splitting reads that have adapters hiding in the middle. it's giving ✂️🧬 and honestly? iconic.

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🎀 SYNOPSIS 🎀

porechop [-h] -i INPUT [-o OUTPUT] [--format
{auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY] [-t THREADS]
[--version] [-b BARCODE_DIR] [--barcode_threshold BARCODE_THRESHOLD]
[--barcode_diff BARCODE_DIFF] [--require_two_barcodes] [--untrimmed]
[--discard_unassigned] [--adapter_threshold ADAPTER_THRESHOLD]
[--check_reads CHECK_READS] [--scoring_scheme SCORING_SCHEME]
[--end_size END_SIZE] [--min_trim_size MIN_TRIM_SIZE] [--extra_end_trim
EXTRA_END_TRIM] [--end_threshold END_THRESHOLD] [--no_split]
[--discard_middle] [--middle_threshold MIDDLE_THRESHOLD]
[--extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE]
[--extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE]
[--min_split_read_size MIN_SPLIT_READ_SIZE]

like yes, that's a lot of brackets, breathe, we'll get through it together 🫶

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🌸 DESCRIPTION 🌸

so basically: Porechop is a tool for finding adapters in Oxford Nanopore reads, trimming them from the ends and splitting reads with internal adapters. that's the whole vibe. adapters in? adapters out. ✨

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💖 OPTIONS 💖

🦋 optional arguments

• -h, --help — shows this help message and then dips. exit stage left. 🚪

👑 Main options

• -i INPUT, --input INPUT — FASTA/FASTQ of input reads, or a directory which will be recursively searched for FASTQ files. this one is required, bestie, no input no output, periodt.
• -o OUTPUT, --output OUTPUT — filename for FASTA or FASTQ of trimmed reads. if you don't set it, the trimmed reads get printed to stdout instead. no pressure. 💅
• --format {auto,fasta,fastq,fasta.gz,fastq.gz} — output format for the reads. if it's auto, the format will be chosen based on the output filename or the input read format (default: auto). she'll figure it out herself, she's smart like that. 🧠✨
• -v VERBOSITY, --verbosity VERBOSITY — level of progress information: 0 = none, 1 = some, 2 = lots, 3 = full. the output will go to stdout if reads are saved to a file and stderr if reads are printed to stdout (default: 1). pick your yap level 🗣️
• -t THREADS, --threads THREADS — number of threads to use for adapter alignment (default: 4). give her more cores, she'll go faster 🔥
• --version — show program's version number and exit. short and sweet, we love a queen who knows herself 💜

🍓 Barcode binning settings

control the binning of reads based on barcodes (i.e. barcode demultiplexing). sorting the girlies into their correct friend groups, fr fr.

• -b BARCODE_DIR, --barcode_dir BARCODE_DIR — reads will be binned based on their barcode and saved to separate files in this directory. incompatible with --output ⚠️ pick a lane, bestie.
• --barcode_threshold BARCODE_THRESHOLD — a read must have at least this percent identity to a barcode to be binned (default: 75.0).
• --barcode_diff BARCODE_DIFF — if the difference between a read's best barcode identity and its second-best barcode identity is less than this value, it will not be put in a barcode bin (to exclude cases which are too close to call) (default: 5.0). she's not gonna guess, that's messy 💀
• --require_two_barcodes — reads will only be put in barcode bins if they have a strong match for the barcode on both their start and end. default behaviour: a read can be binned with a match at its start or end. stricter queen energy 👑
• --untrimmed — bin reads but do not trim them (appropriate if reads are to be used with Nanopolish). default is to trim the reads. sometimes you keep the whole fit on, iykyk 🎀
• --discard_unassigned — discard unassigned reads (instead of creating a "none" bin) (default: False). no bin, no home, no problem 🙈

🌈 Adapter search settings

control how the program determines which adapter sets are present.

• --adapter_threshold ADAPTER_THRESHOLD — an adapter set has to have at least this percent identity to be labelled as present and trimmed off (0 to 100) (default: 90.0).
• --check_reads CHECK_READS — this many reads will be aligned to all possible adapters to determine which adapter sets are present (default: 10000). she does her research first, obviously 📚
• --scoring_scheme SCORING_SCHEME — comma-delimited string of alignment scores: match, mismatch, gap open, gap extend (default: 3,-6,-5,-2). yes those are negatives, no we're not scared of them 🫶

💅 End adapter settings

control the trimming of adapters from read ends. snip snip ✂️

• --end_size END_SIZE — the number of base pairs at each end of the read which will be searched for adapter sequences (default: 150).
• --min_trim_size MIN_TRIM_SIZE — adapter alignments smaller than this will be ignored (default: 4). tiny matches don't count, we don't do micro-drama 🙅
• --extra_end_trim EXTRA_END_TRIM — this many additional bases will be removed next to adapters found at the ends of reads (default: 2).
• --end_threshold END_THRESHOLD — adapters at the ends of reads must have at least this percent identity to be removed (0 to 100) (default: 75.0).

🧚 Middle adapter settings

control the splitting of read from middle adapters. the drama in the middle of the read, we handle it ✨

• --no_split — skip splitting reads based on middle adapters. default: split reads when an adapter is found in the middle. sometimes you just let it be, no cap.
• --discard_middle — reads with middle adapters will be discarded. default: reads with middle adapters are split. note that this option is on by default when outputting reads into barcode bins 👀
• --middle_threshold MIDDLE_THRESHOLD — adapters in the middle of reads must have at least this percent identity to be found (0 to 100) (default: 85.0).
• --extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE — this many additional bases will be removed next to middle adapters on their "good" side (default: 10). good side stays winning 💖
• --extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE — this many additional bases will be removed next to middle adapters on their "bad" side (default: 100). the bad side gets the big chop 😭
• --min_split_read_size MIN_SPLIT_READ_SIZE — post-split read pieces smaller than this many base pairs will not be outputted (default: 1000). too smol, no thanks 🍓

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⭐ AUTHOR ⭐

this manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. thank you andreas, we appreciate you 🫶

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and that's the whole page, bestie!! you read all of it, that's main character energy fr fr 💅✨

this was porechop version 0.2.3, from August 2018, living under the PORECHOP(1) name 💜 bye bye, go trim some adapters 🧬✂️🎀