VELVETH(1)

💖 VELVETH(1) 💖

okay bestie, sit down, hydrate, because we're talking about velveth — a simple hashing program ✨ (that's what it calls itself, and honestly? humble queen behavior). It lives in the User Commands section, and its full glow-up name is Version 1.2.09.

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🌸 NAME 🌸

velveth — a simple hashing program 🧚

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🦋 DESCRIPTION 🦋

So basically: velveth is a simple hashing program, Version 1.2.09. That's the whole vibe. She hashes. She's simple. She's iconic. 💅

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✨ OPTIONS ✨

Every single one of these defaults to off, no cap:

• -strand_specific — turn this on for strand specific transcriptome sequencing data (default: off) 🧬
• -reuse_Sequences — reuse a Sequences file (or link) that's already chillin' in the directory, so you don't have to hand over the original filenames in this case (default: off) ♻️
• -reuse_binary — reuse the binary sequences file (or link) that's already in the directory, again meaning you do not need to provide the original filenames in this case (default: off) ♻️
• -noHash — just prepare the Sequences file and dip; do not hash reads, and do not prepare a Roadmaps file (default: off) 🙈
• -create_binary — create a binary CnyUnifiedSeq file (default: off) 🔥

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🎀 OPTIONS — Synopsis 🎀

the receipts, bestie 👑

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 are picked up by graph, so please leave them there 🫶 don't move them, don't rename them, don't touch them. Just let them live.

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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. (read it again. there is NO warranty. none. zero. nada. 😭)

Compilation settings: CATEGORIES = 2 MAXKMERLENGTH = 31

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🌈 COPYRIGHT — Usage 🌈

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

directory

the directory name for output files 📁

hash_length

EITHER an odd integer (if it's even, it will be decremented) that's <= 31 (if it's above, it will be reduced) — OR — m,M,s where m and M are odd integers (if they're not odd, they will be decremented) with m < M <= 31 (if 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

the path to a sequence file, or - for standard input 🍓

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🌸 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 🫧

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

• -interleaved — the file contains paired reads interleaved in the one file (this is the default) 🌈
• -separate — read 2 separate files for paired reads ✌️

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⭐ Read type options: ⭐

-short  -shortPaired

-short2 -shortPaired2

-long   -longPaired

-reference

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and that's the whole page, bestie 🎀 this was velveth 1.2.10+dfsg1, dated July 2018, from the VELVETH(1) era. go forth and hash responsibly 💖✨