VELVETG_127_LONG(1)

💖 VELVETG_127_LONG — bestie edition 💖

okay so. velvetg_127_long is the whole de Bruijn graph construction, error removal and repeat resolution situation, and this particular build is compiled with MAXKMERLENGTH = 127 and LONGSEQUENCES turned on. it's giving assembly main character energy, no cap. 🦋

✨ DESCRIPTION ✨

so the way you run it is literally just:

./velvetg directory [options]

• directory — the working directory name. that's it, that's the whole positional argument. 🎀

🌸 Standard options 🌸

these are the ones you'll actually be reaching for, bestie.

• -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> — 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 🔥

this is where it gets spicy. buckle up. 🫶

• -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> — est. standard deviation of the respective dataset. default: 10% of corresponding length. and yes, the note says: replace * by nothing, 2 or _long as necessary. so like, pick your fighter. ⭐
• -scaffolding <yes|no> — scaffolding of contigs using 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 into 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. heads up bestie: this means no recalculation possible. default: no. 💀
• -paired_exp_fraction <double> — remove 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, 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 🎀

here's the loot you get when it's done slaying:

• 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.

ngl, the -very_clean thing is not a vibe if you ever wanna recalculate. read the label, babes. 🙈

okay that's the whole page, you ate it, you understood it, iconic behavior. this was velvetg_127_long version 1.2.10+dfsg1, dated July 2018 — love her, respect her, cite her. periodt. 👑🌈💜