VELVETG_127(1)

👑 VELVETG_127 — the manual, but make it cute

okay bestie, listen. this is velvetg_127 from the User Commands section of the manual (section 1, iykyk), and it's the one that does de Bruijn graph construction, error removal and repeat resolution, with MAXKMERLENGTH = 127. that's the whole vibe. 127 is a lot of kmer and she is NOT shy about it 💅

🌸 SYNOPSIS 🌸

./velvetg directory [options]

✨ DESCRIPTION ✨

so basically you run it like this: ./velvetg directory [options], and here's what the pieces mean:

• directory — the working directory name. that's it. that's the whole required argument. she needs a home 🏠

🎀 Standard options (the main-character ones)

• -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 the assembly. (default: no tracking)
• -min_contig_lgth <integer> — minimum contig length that gets exported to the contigs.fa file. (default: hash length * 2)
• -amos_file <yes|no> — export the 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 (for when you're feeling brave)

• -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 the corresponding length)

[replace '*' by nothing, '2' or '_long' as necessary] — fr fr, the * is a placeholder, swap it out properly 🙈

• -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> — 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. (default: no)

⚠️ heads up bestie: with -very_clean, no recalculation is possible. she said goodbye and she meant it 💀

• -paired_exp_fraction <double> — remove all the paired end connections which [have] 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 (the lil gifts she leaves behind)

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

💖 the sign-off 💖

and that's the whole page, bestie. this version is velvetg_127 1.2.10+dfsg1, dated July 2018 — a whole icon, aging like fine wine 🍷 no cap, go build your graphs and slay. periodt. 🫶✨