FLEXBAR(1)

✨ FLEXBAR(1) ✨

User Commands — ok bestie, gather round, we're talking about flexbar(1) 💅

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🌸 NAME 🌸

flexbar — the flexible barcode and adapter removal situation for sequencing platforms. it's giving ✨cleanup era✨

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🎀 SYNOPSIS 🎀

flexbar -r reads [-t target] [-b barcodes] [-a adapters] [options]

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🦋 DESCRIPTION 🦋

okay so Flexbar preprocesses high-throughput sequencing data efficiently, no cap. it demultiplexes barcoded runs AND removes adapter sequences. and that's not all — trimming and filtering features are provided too 🫶. Flexbar increases mapping rates and improves genome and transcriptome assemblies. it supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform. iconic behavior honestly 👑

⚠️ bestie listen — parameter names changed in Flexbar. Please review scripts. do not just run your old script and expect the vibes to be the same, i am begging 🙈

the recent months, default settings were optimised, several bugs were fixed and various improvements were made, e.g. revamped command-line interface, new trimming modes as well as lower time and memory requirements. glow up fr fr ✨

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💖 the tiny little flags that just print stuff 💖

• -h, --help — displays this help message. your girl's your girl's help. 🎀
• -w, --advanced — print advanced options help screen. there's MORE. always more. 💀
• -i, --cite — show program reference for citation. cite her, she worked hard. 📚

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🌈 Basic options:

• -n, --threads NUM — number of threads to employ. Default: 1. give her more threads, she'll give you more speed 🧚
• -t, --target STR — prefix for output file names or paths. Default: flexbar. name your children 🥺
• -r, --reads FILE — Fasta/q file or stdin (-) with reads that may contain barcodes. the main character input fr.
• -p, --reads2 FILE — second input file of paired reads, gz and bz2 files supported. the plus one 💞
• -f, --format STR — quality format: sanger, solexa, i1.3, i1.5, i1.8 (illumina 1.8+). pick your era, bestie 🕰️
• -c, --color-space — input in color-space format csfasta or csfastq in sanger scaling. 🌈 retro vibes

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💜 Barcode detection:

• -b, --barcodes FILE — Fasta file with barcodes for demultiplexing that may contain N. 🏷️
• -br, --barcode-reads FILE — Fasta/q file composed of separate barcode reads for detection. 🧬
• -be, --barcode-trim-end STR — type of detection, see section trim-end modes. Default: ANY.
• -bo, --barcode-min-overlap NUM — minimum overlap of barcode and read. Default: barcode length.
• -bt, --barcode-threshold NUM — allowed mismatches and gaps per 10 bases overlap. Default: 1.0.
• -bu, --barcode-unassigned — include unassigned reads in output generation. nobody gets left out in this house 🫶

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💅 Adapter removal:

• -a, --adapters FILE — Fasta file with adapters for removal that may contain N. bye adapter 👋
• -as, --adapter-seq STR — single adapter sequence as alternative to adapters option. one adapter, one moment, one vibe ✨
• -ae, --adapter-trim-end STR — type of removal, see section trim-end modes. Default: RIGHT.
• -ao, --adapter-min-overlap NUM — minimum overlap of adapter and read sequence. Default: 1.
• -at, --adapter-threshold NUM — allowed mismatches and gaps per 10 bases overlap. Default: 3.0.

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🍓 Filtering and trimming:

• -u, --max-uncalled NUM — allowed uncalled bases (N or .) for each read. Default: 0.
• -x, --pre-trim-left NUM — trim given number of bases on 5' read end before detection. ✂️
• -y, --pre-trim-right NUM — trim specified number of bases on 3' end prior to detection. ✂️
• -q, --pre-trim-phred NUM — trim 3' end until specified or higher quality reached. quality queen check ✅
• -k, --post-trim-length NUM — trim to specified read length from 3' end after removal. 📏
• -m, --min-read-length NUM — minimum read length to remain after removal. Default: 18. short king? rejected. 💀

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👑 Output selection:

• -o, --fasta-output — prefer non-quality formats fasta and csfasta for output.
• -z, --zip-output STR — enable direct compression of output files. One of GZ and BZ2. zip it, lock it, slay it 🔒
• -s, --single-reads — write single paired reads for too short counterparts. keep the lonely ones too 🥺

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🧚 Logging and tagging:

• -l, --log-level STR — print valid optimal read alignment. One of ALL, MOD, and TAB.
• -g, --removal-tags — tag reads that are subject to adapter or barcode removal. 🏷️✨

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💫 Trim-end modes:

okay this is the part everyone skips and then everyone is confused, so READ IT bestie 😭

• ANY: longer side of read remains after removal of overlap
• LEFT: right side remains after removal, align <= read end
• RIGHT: left part remains after removal, align >= read start
• LEFT_TAIL: consider first n bases of reads in alignment
• RIGHT_TAIL: use only last n bases, see tail-length options

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🔥 EXAMPLES 🔥

look at her go:

flexbar -r reads.fq -f i1.8 -t target -b brc.fa -a adap.fa
flexbar -r reads.csfastq.gz -a adap.fa -ao 5 -ae LEFT -c

copy them exactly, no improvising bestie, this is not jazz 🎷

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⭐ VERSION ⭐

flexbar version: 2.4 Last update July 29, 2013

Advanced options: flexbar -w

flexbar version 2.4

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and that's the whole page 🫶 flexbar version 2.4, born January 2014, part of the FLEXBAR(1) manual family — she's an icon, she's a legend, and she is the moment. go trim something, bestie. periodt. 💖✨🎀