BIO-RAINBOW(1)

💖 NAME 💖

bio-rainbow — clustering and assembling short reads for bioinformatics, bestie 💅

✨ SYNOPSIS ✨

rainbow <cmd> [options]

🦋 DESCRIPTION 🦋

okay so. this is rainbow 2.0.4 — the whole vibe is <ruanjue@gmail.com, chongzechen@gmail.com> ✨

It's giving: you pick a <cmd> and it does the thing. There are three commands and they are lowkey iconic. Let's go one by one, no skips, no cap 🫶

🌸 cluster 🌸

Input File Format: paired fasta/fastq file(s) Output File Format: <seqid:int>\t<cluster_id:int>\t<read1:string>\t<read2:string>

• -1 <string> — input fasta/fastq file. and yes, it supports multiple -1 💖
• -2 <string> — input fasta/fastq file, supports multiple -2 [null]
• -l <int> — read length. default: 0 variable
• -m <int> — maximum mismatches [4]
• -e <int> — exactly matching threshold [2000]
• -L — low level of polymorphism

💜 div 💜

Input File Format: <seqid:int>\t<cluster_id:int>\t<read1:string>\t<read2:string> Output File Format: <seqid:int>\t<cluster_id:int>\t<read1:string>\t<read2:string>[\t<pre_cluster_id:int>]

• -i <string> — input file [stdin]
• -o <string> — output file [stdout]
• -k <int> — K_allele, min variants to create a new group [2]
• -K <int> — K_allele, divide regardless of frequency when num of variants exceed this value [50]
• -f <float> — frequency, min variant frequency to create a new group [0.2]

🎀 merge 🎀

Input File Format: <seqid:int>\t<cluster_id:int>\t<read1:string>\t<read2:string>[\t<pre_cluster_id:int>]

• -i <string> — input rbasm output file [stdin]
• -a — output assembly 👑
• -o <string> — output file for merged contigs, one line per cluster [stdout]
• -N <int> — maximum number of divided clusters to merge [300]
• -l <int> — minimum overlap when assemble two reads (valid only when -a is opened) [5]
• -f <float> — minimum fraction of similarity when assembly (valid only when -a is opened) [0.90]
• -r <int> — minimum number of reads to assemble (valid only when -a is opened) [5]
• -R <int> — maximum number of reads to assemble (valid only when -a is opened) [300]

bestie the -a flags in merge literally do nothing unless you open -a first. it's giving "you have to say please". remember that 😭

🌈 AUTHOR 🌈

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🫶

and that's the whole page, fr fr 💖 this was bio-rainbow 2.0.4, dated July 2018 — periodt, mwah 🎀✨💅