VELVETH_127_LONG(1)

🌸 VELVETH_127_LONG 💅

okay bestie, so this is velveth_127_long(1), a User Commands page, and the manual name up top is literally VELVETH_127_LONG(1) — yes it's a whole mouthful, we love a dramatic name. 🎀

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✨ NAME ✨

velveth_127_long — it's a simple hashing program, but make it MAXKMERLENGTH = 127 and LONGSEQUENCES. no cap, that's the whole vibe. 🦋

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💖 DESCRIPTION 💖

velveth — simple hashing program, Version 1.2.09. that's it, that's the sentence, she's short and she knows it. ✨

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🌈 OPTIONS 🌈

• -strand_specific — for strand specific transcriptome sequencing data. default: off. turn it on only if that's your situation, iykyk 💅
• -reuse_Sequences — reuse the Sequences file (or link) that's already chillin' in the directory. if you do this you do not need to hand over the original filenames. default: off 🫶
• -reuse_binary — reuse the binary sequences file (or link) that's already in the directory. again, no original filenames required in this case. default: off ✨
• -noHash — simply prepare the Sequences file. do not hash reads, do not prepare a Roadmaps file. default: off 🙈
• -create_binary — create a 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 are picked up by graph, so please leave them there] — like, do not move them, bestie, they have a job. 😭

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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. (yes the NO is in caps in the original too, she's yelling and she's valid 💅)

Compilation settings: CATEGORIES = 2 MAXKMERLENGTH = 127 OPENMP LONGSEQUENCES

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 you hand it an even one, it will be decremented) <= 127 (if you go 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 <= 127 (if above, 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 🫶

🌈 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 — File contains paired reads interleaved in the one file. this is the default 💅
• -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!! 🫶 this is velveth_127_long version 1.2.10+dfsg1, dated July 2018 — go forth and hash, main character. 👑💖