VELVETG(1)

💖 NAME 💖

velvetg — building de Bruijn graphs, yeeting errors out of them, and resolving repeats, bestie 🧬✨

🌸 DESCRIPTION 🌸

okay so here's the whole vibe. You run it like this:

Usage: ./velvetg directory [options]

and directory is just... the working directory name. that's it. that's the girl 💅

🎀 Standard options:

• -cov_cutoff <floating-point|auto> — removes low coverage nodes AFTER tour bus, or you can let the system infer it for you. (default: no removal) 🫶
• -ins_length <integer> — the expected distance between two paired end reads. (default: no read pairing)
• -read_trkg <yes|no> — tracking of short read positions in assembly. (default: no tracking) 👀
• -min_contig_lgth <integer> — minimum contig length exported to the contigs.fa file. (default: hash length * 2)
• -amos_file <yes|no> — export assembly to an AMOS file. (default: no export)
• -exp_cov <floating point|auto> — expected coverage of unique regions, or let the system infer it. (default: no long or paired-end read resolution)
• -long_cov_cutoff <floating-point> — removal of nodes with low long-read coverage AFTER tour bus. (default: no removal)

✨ Advanced options:

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

bestie real talk: you replace the '*' with nothing, '2' or '_long' as necessary. iykyk 🧚

• -scaffolding <yes|no> — scaffolding of contigs used paired end information. (default: on)
• -max_branch_length <integer> — maximum length in base pair of bubble. (default: 100)
• -max_divergence <floating-point> — maximum divergence rate between two branches in a bubble. (default: 0.2)
• -max_gap_count <integer> — maximum number of gaps allowed in the alignment of the two branches of a bubble. (default: 3)
• -min_pair_count <integer> — minimum number of paired end connections to justify the scaffolding of two long contigs. (default: 5)
• -max_coverage <floating point> — removal of high coverage nodes AFTER tour bus. (default: no removal)
• -coverage_mask <int> — minimum coverage required for confident regions of contigs. (default: 1)
• -long_mult_cutoff <int> — minimum number of long reads required to merge contigs. (default: 2)
• -unused_reads <yes|no> — export unused reads in the UnusedReads.fa file. (default: no)
• -alignments <yes|no> — export a summary of contig alignment to the reference sequences. (default: no)
• -exportFiltered <yes|no> — export the long nodes which were eliminated by the coverage filters. (default: no)
• -clean <yes|no> — remove all the intermediary files which are useless for recalculation. (default : no)
• -very_clean <yes|no> — remove all the intermediary files (no recalculation possible). (default: no)

⚠️ no cap, -very_clean means recalculation is off the table. it's giving point of no return 💀

• -paired_exp_fraction <double> — remove all the paired end connections which less than the specified fraction of the expected count. (default: 0.1)
• -shortMatePaired* <yes|no> — for mate-pair libraries, indicate that the library might be contaminated with paired-end reads. (default no)
• -conserveLong <yes|no> — preserve sequences with long reads in them. (default no)

👑 Output:

• directory/contigs.fa — fasta file of contigs longer than twice hash length 🌈
• directory/stats.txt — stats file (tab-spaced) useful for determining appropriate coverage cutoff 📊
• directory/LastGraph — special formatted file with all the information on the final graph 🕸️
• directory/velvet_asm.afg — (if requested) AMOS compatible assembly file

and that's the whole page, bestie!! velvetg version 1.2.10+dfsg1, dated July 2018 — go build some graphs, you absolute icon 💖✨🦋🎀