VELVETH_127(1)

👑 VELVETH_127 — like, the manual page bestie 💅

okay so welcome to velveth_127, a User Commands era icon ✨ (yes it lives in section 1, she's a command, she's that girl)

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🌸 NAME 🌸

velveth_127 — simple hashing program (MAXKMERLENGTH = 127)

no cap, that's the whole name. short, sweet, iconic.

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🦋 DESCRIPTION 🦋

velveth — simple hashing program, Version 1.2.09 🎀

that's it. that's the description. she doesn't over-explain, she just is.

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💖 OPTIONS 💖

• -strand_specific — for strand specific transcriptome sequencing data (default: off) 🧬
• -reuse_Sequences — reuse Sequences file (or link) already in directory (no need to provide original filenames in this case (default: off) 🫶
• -reuse_binary — reuse binary sequences file (or link) already in directory (no need to provide original filenames in this case (default: off) 💜
• -noHash — simply prepare Sequences file, do not hash reads or prepare Roadmaps file (default: off) 🙈
• -create_binary — create binary CnyUnifiedSeq file (default: off) 💀

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🌈 Synopsis 🌈

bestie, these are the actual invocations, copy them EXACTLY, i'm not playing 😭

• 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

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✨ Output ✨

directory/Roadmaps directory/Sequences

[Both files are picked up by graph, so please leave them there] 🫶 like. do NOT move them. graph needs them. leave the babies alone.

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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. 😭 (she said what she said)

Compilation settings: CATEGORIES = 2 MAXKMERLENGTH = 127 OPENMP 🔥

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💅 Usage 💅

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

🌸 the args, explained 🌸

• directory — directory name for output files 📁
• hash_length — EITHER an odd integer (if even, it will be decremented) <= 127 (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 <= 127 (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) 💜

• -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 💅✨

this was velveth_127 version 1.2.10+dfsg1, dated July 2018 — mwah, go hash something gorgeous 🎀🦋💖