VELVETH_63_LONG(1)

💖 NAME 💖

okay bestie, welcome to VELVETH_63_LONG(1) — the manual page for velveth_63_long, a simple hashing program (MAXKMERLENGTH = 63, LONGSEQUENCES). She's here to hash, she's here to prep, and she's lowkey iconic. 💅

✨ DESCRIPTION ✨

velveth — simple hashing program Version 1.2.09. That's the whole description, bestie. Periodt. 🫶

🌸 OPTIONS 🌸

These are the main-character switches, okay? They all default to off unless said otherwise.

• -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). ✨

📚 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] 🙈

👑 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 = 63 OPENMP LONGSEQUENCES. 🌈

🛠️ Usage 🛠️

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) <= 63 (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 <= 63 (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. 🧚

📁 File format options 📁

• -fasta — file format option. 🌸
• -fastq — file format option. 🌸
• -raw — file format option. 🌸
• -fasta.gz — file format option. 🌸
• -fastq.gz — file format option. 🌸
• -raw.gz — file format option. 🌸
• -sam — file format option. 🌸
• -bam — file format option. 🌸
• -fmtAuto — file format option. (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 (default). 💖
• -separate — Read 2 separate files for paired reads. 🦋

🌈 Read type options 🌈

• -short — read type option. ✨
• -shortPaired — read type option. ✨
• -short2 — read type option. ✨
• -shortPaired2 — read type option. ✨
• -long — read type option. ✨
• -longPaired — read type option. ✨
• -reference — read type option. ✨

okay bye bestie, this page was brought to you by velveth_63_long 1.2.10+dfsg1, dated July 2018 — mwah 💋