VELVETH_DE(1)

🌸 VELVETH_DE — the manual page, bestie edition 🌸

okay so this is velveth_de from section 1 of the manual (User Commands, we love a classic) 💖 it's the colorspace version of velveth, and honestly? she's a whole vibe. let's get into it.

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✨ NAME ✨

velveth_de — simple hashing program (colorspace version) 🦋

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🎀 DESCRIPTION 🎀

velveth — simple hashing program, Version 1.2.09. that's it, that's the description. short, sweet, main character energy, no notes 💅

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💅 OPTIONS 💅

• -strand_specific — for strand specific transcriptome sequencing data. default: off ✨
• -reuse_Sequences — reuse a Sequences file (or link) that's already chillin' in the directory. in that case you do NOT need to provide the original filenames. default: off 💖
• -reuse_binary — reuse a binary sequences file (or link) that's already in the directory. again, no need to hand over the original filenames here. default: off 🧚
• -noHash — just prepare the Sequences file, periodt. do not hash reads, do not prepare a Roadmaps file. default: off 🌸
• -create_binary — create a binary CnyUnifiedSeq file. default: off ⭐

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🦋 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 are picked up by graph, so please leave them there 🫶 like genuinely do not move them, bestie, graph needs them exactly where they are.

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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. (dramatic but true, she said it herself 😭)

Compilation settings: CATEGORIES = 2 MAXKMERLENGTH = 31 OPENMP COLOR 🌈

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🌟 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 (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, they will be decremented) with m < M <= 31 (if above, they 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 ⭐

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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 💜 go forth and hash, you've got this 👑✨

signing off from velveth_de version 1.2.10+dfsg1, dated July 2018 — yeah she's vintage but she still slays 💅🎀