VELVETH_63(1)

💖 VELVETH_63 — bestie's guide to the hashing program 💖

okay so real talk, this is the manual page for velveth_63 — that's the simple hashing program build where MAXKMERLENGTH = 63. It's the velveth family, and it is SO iconic, we're gonna walk through every single flag together, no skipping, no cap. 🫶

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✨ NAME ✨

velveth_63 — simple hashing program (MAXKMERLENGTH = 63) 💅

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🌸 DESCRIPTION 🌸

velveth — simple hashing program Version 1.2.09. That's it, that's the vibe. She hashes. She's simple. She's booked and busy. ✨

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🎀 OPTIONS 🎀

• -strand_specific — for strand specific transcriptome sequencing data (default: off). Only turn her on if that's your situation, bestie. 🧬
• -reuse_Sequences — reuse the Sequences file (or link) that's already sitting in the directory. And because it's already there, you do NOT need to hand over the original filenames (default: off). recycling queen 🍓
• -reuse_binary — reuse the binary sequences file (or link) already in the directory, and again, no need to provide the original filenames in this case (default: off). 🦋
• -noHash — literally just prepare the Sequences file. Do NOT hash reads, do NOT prepare a Roadmaps file (default: off). She's doing the bare minimum and honestly? valid. 💀
• -create_binary — create the binary CnyUnifiedSeq file (default: off). 🔥

⭐ Synopsis ⭐

Short single end reads

velveth Assem 29 -short -fastq s_1_sequence.txt

Paired-end short reads (remember to interleave paired reads!)

velveth Assem 31 -shortPaired -fasta interleaved.fna

Paired-end short reads (using separate files for the paired reads)

velveth Assem 31 -shortPaired -fasta -separate left.fa right.fa

Two channels and some long reads

velveth Assem 43 -short -fastq unmapped.fna -longPaired -fasta SangerReads.fasta

Three channels

velveth Assem 35 -shortPaired -fasta pe_lib1.fasta -shortPaired2 pe_lib2.fasta -short3 se_lib1.fa

👑 Output 👑

directory/Roadmaps
directory/Sequences

BOTH files get picked up by graph, so PLEASE leave them right where they are. Do not move them. Do not rename them. Do not touch them. 🚫

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💜 COPYRIGHT 💜

Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)

This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Compilation settings: CATEGORIES = 2, MAXKMERLENGTH = 63, OPENMP

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🌈 USAGE & ARGUMENTS 🌈

Usage: ./velveth directory hash_length
{[-file_format][-read_type][-separate|-interleaved] filename1 [filename2 ...]} {...} [options]

• directory — directory name for output files 📁
• hash_length — EITHER an odd integer (and if it's even, it will be decremented) that is <= 63 (and if it's above, it will be reduced) : OR : m,M,s where m and M are odd integers (if they're not, they get decremented) with m < M <= 63 (if M is above, it will be reduced), and s is a step (an even number). Velvet will then hash from k=m to k=M with a step of s. 🎯
• filename — path to sequence file, or - for standard input. yes, - is the main character here. 📥

🧚 File format options 🧚

• -fasta
• -fastq
• -raw
• -fasta.gz
• -fastq.gz
• -raw.gz
• -sam
• -bam
• -fmtAuto

(Note: -fmtAuto will detect fasta or fastq, and will try the following programs for decompression: gunzip, pbunzip2, bunzip2)

💅 File layout options for paired reads (only for fasta and fastq formats) 💅

• -interleaved — the file contains paired reads interleaved in the one file (default). one file, two reads, we love a two-for-one. 🫶
• -separate — read 2 separate files for paired reads. ✌️

🌸 Read type options 🌸

• -short, -shortPaired
• -short2, -shortPaired2
• -long, -longPaired
• -reference

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and that's the whole page, bestie, we got every last flag, every default, every example, all of it. 💖

velveth_63 — version 1.2.10+dfsg1, dated July 2018. mwah, bye. 💅✨🎀