VELVETH_LONG(1)

💖 VELVETH_LONG(1) — the long-sequences edition, bestie 💖

User Commands · so this is the velveth_long page, the LONGSEQUENCES build of velveth, okay? Buckle up.

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✨ NAME ✨

velveth_long — simple hashing program (LONGSEQUENCES)

🌸 DESCRIPTION 🌸

velveth — simple hashing program Version 1.2.09

no cap that's the whole description. iconic.

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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, so you don't have to hand over the original filenames in this case (default: off)
• -reuse_binary — reuse a binary sequences file (or link) that's already in the directory, so again no original filenames needed here (default: off)
• -noHash — just prepare the Sequences file, don't hash reads and don't prepare a Roadmaps file (default: off)
• -create_binary — create a binary CnyUnifiedSeq file (default: off)

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🦋 Synopsis 🦋

okay so here's the vibe, one example at a time:

• Short single end reads:

velveth Assem 29 -short -fastq s_1_sequence.txt

• Paired-end short reads (and remember to interleave those paired reads, bestie):

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

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⭐ Output ⭐

directory/Roadmaps directory/Sequences

🫶 Both files are picked up by graph, so please leave them there! Don't be moving them, fr fr.

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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 = 31 OPENMP LONGSEQUENCES

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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 even, it will be decremented) <= 31 (if above, will be reduced) : OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 31 (if above, will be reduced)

and s is a step (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, iykyk)

• -interleaved — File contains paired reads interleaved in the one file (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, you ate that 💅✨ this one's velveth_long version 1.2.10+dfsg1, dated July 2018 — love you, go hash something pretty 🦋💖