VELVETG_DE(1)

💖 VELVETG_DE — the de Bruijn graph glow-up 💖

okay bestie, listen. this is velvetg_de, a User Commands girly from the velvetg_de(1) manual page. she does de Bruijn graph construction, error removal and repeat resolution — but the colorspace version, so she's got a whole different flavor. and honestly? she ate. 🦋

✨ NAME ✨

velvetg_de — de Bruijn graph construction, error removal and repeat resolution (colorspace version)

🌸 DESCRIPTION 🌸

here's how you slide into her DMs:

Usage: ./velvetg directory [options]

• directory — 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 let the system infer it all by itself. (default: no removal) — she's lowkey respectful like that.
• -ins_length <integer> — the expected distance between two paired end reads. (default: no read pairing) 💀 no pairing, no party.
• -read_trkg <yes|no> — tracks short read positions in the assembly. (default: no tracking) — she's not a stalker unless you ask.
• -min_contig_lgth <integer> — 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> — expected coverage of unique regions, or let the system infer it for you. (default: no long or paired-end read resolution) — trusting the system is very main character energy fr fr.
• -long_cov_cutoff <floating-point> — removal of nodes with low long-read coverage, and this happens 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> — the estimated standard deviation of the respective dataset. (default: 10% of corresponding length)

real talk: you gotta replace '*' by nothing, '2' or '_long' as necessary. iykyk. 💅

• -scaffolding <yes|no> — scaffolding of contigs using paired end information. (default: on) — she's on by default, periodt.
• -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 needed 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> — 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) 😭 gone but not forgotten.
• -clean <yes|no> — removes all the intermediary files which are useless for recalculation. (default : no)
• -very_clean <yes|no> — removes all the intermediary files. (default: no)

⚠️ bestie be so serious rn: with -very_clean there is no recalculation possible. she said what she said. 🩷

• -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, this indicates that the library might be contaminated with paired-end reads. (default no)
• -conserveLong <yes|no> — preserves 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) that's useful for determining the appropriate coverage cutoff.
• directory/LastGraph — a special formatted file with all the information on the final graph. the whole lore, basically. 📖
• directory/velvet_asm.afg — (if requested) the AMOS compatible assembly file.

and that's the whole page, bestie — every flag, every default, every file, nothing skipped, no cap. 🫶

this gorgeous thing is velvetg_de 1.2.10+dfsg1, and she dropped in July 2018. slay, happy assembling, mwah 💅✨💖