VELVETG_LONG(1)

💖 NAME 💖

velvetg_long — building de Bruijn graphs, yeeting errors, and untangling repeats, but make it LONGSEQUENCES ✨

🌸 DESCRIPTION 🌸

Okay bestie, listen. This is the long-read era of velvetg and it's so much. Usage looks like this, exactly:

./velvetg directory [options]

And directory is just:

• directory — the working directory name, that's it, that's the whole vibe 🎀

✨ Standard options ✨

These are the everyday ones, the main characters 👑

• -cov_cutoff <floating-point|auto> — removes low coverage nodes AFTER tour bus, or lets the system infer the cutoff itself. Default: no removal 🙈
• -ins_length <integer> — the expected distance between two paired end reads. Default: no read pairing 💔
• -read_trkg <yes|no> — tracks where short reads sit in the assembly. Default: no tracking 🕵️♀️
• -min_contig_lgth <integer> — the minimum contig length that gets exported to the contigs.fa file. Default: hash length * 2 📏
• -amos_file <yes|no> — exports the assembly to an AMOS file. Default: no export 📦
• -exp_cov <floating point|auto> — the expected coverage of unique regions, or let the system infer it. Default: no long or paired-end read resolution 🔮
• -long_cov_cutoff <floating-point> — removes nodes with low long-read coverage AFTER tour bus. Default: no removal ✂️

🔥 Advanced options 🔥

The deep lore. Buckle up, we're going in 💅

• -ins_length* <integer> — the expected distance between two paired-end reads in the respective short-read dataset. Default: no read pairing 🧬
• -ins_length_long <integer> — the expected distance between two long paired-end reads. Default: no read pairing 🦋
• -ins_length*_sd <integer> — the estimated standard deviation of the respective dataset. Default: 10% of corresponding length 📐

Heads up: replace '*' by nothing, '2' or '_long' as necessary ⭐

• -scaffolding <yes|no> — scaffolding of contigs using paired end information. Default: on 🏗️
• -max_branch_length <integer> — maximum length in base pair of a bubble. Default: 100 🫧
• -max_divergence <floating-point> — the maximum divergence rate between two branches in a bubble. Default: 0.2 🍓
• -max_gap_count <integer> — the maximum number of gaps allowed when aligning the two branches of a bubble. Default: 3 🕳️
• -min_pair_count <integer> — the minimum number of paired end connections needed to justify scaffolding two long contigs. Default: 5 🤝
• -max_coverage <floating point> — removes high coverage nodes AFTER tour bus. Default: no removal 🚫
• -coverage_mask <int> — the minimum coverage required for confident regions of contigs. Default: 1 🎭
• -long_mult_cutoff <int> — the minimum number of long reads required to merge contigs. Default: 2 🔗
• -unused_reads <yes|no> — exports unused reads into the UnusedReads.fa file. Default: no 🗑️
• -alignments <yes|no> — exports a summary of contig alignment to the reference sequences. Default: no 🧭
• -exportFiltered <yes|no> — exports the long nodes that got eliminated by the coverage filters. Default: no 👻
• -clean <yes|no> — removes all the intermediary files that are useless for recalculation. Default: no 🧹
• -very_clean <yes|no> — removes all the intermediary files, which means no recalculation possible. Default: no 💀
• -paired_exp_fraction <double> — removes all the paired end connections which are less than the specified fraction of the expected count. Default: 0.1 🎯
• -shortMatePaired* <yes|no> — for mate-pair libraries, indicates that the library might be contaminated with paired-end reads. Default: no 🧫
• -conserveLong <yes|no> — preserves sequences that have long reads in them. Default: no 🌿

🎀 Output 🎀

Here's what you get when the whole thing slays 💖

• directory/contigs.fa — fasta file of contigs longer than twice hash length 🧬
• directory/stats.txt — stats file (tab-spaced) that's genuinely useful for determining the appropriate coverage cutoff 📊
• directory/LastGraph — a special formatted file holding all the information on the final graph 🌐
• directory/velvet_asm.afg — (if requested) the AMOS compatible assembly file 🗂️

That's the whole page bestie, no cap. This was velvetg_long version 1.2.10+dfsg1, dated July 2018 — go forth and assemble, you absolute icon 💅✨🫶