VELVETG_63(1)

💖 VELVETG_63 💖

okay so bestie, welcome to velvetg_63 — it's the de Bruijn graph construction, error removal and repeat resolution girlie, and this build is the MAXKMERLENGTH = 63 one. section 1, user commands, she's a whole icon. 🦋

✨ NAME ✨

velvetg_63 — de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 63) 👑

🌸 DESCRIPTION 🌸

the vibe is literally just this:

Usage: ./velvetg directory [options]

and directory is the working directory name, periodt. that's the whole teaser. now let's get into the options because there are so many and every single one of them matters 💅

🎀 Standard options: 🎀

• -cov_cutoff <floating-point|auto> — removes low coverage nodes AFTER tour bus, or you can let the system infer it for you (main character behaviour honestly). 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> — the 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 (she's independent 💅). 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> — est. standard deviation of the respective dataset. default: 10% of corresponding length. also, side note: replace '*' by nothing, '2' or '_long' as necessary 🫶
• -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 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> — 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 (no recalculation possible 😭). default: no.

bestie. -very_clean means no recalculation possible. it is giving irreversible. proceed with the awareness of a main character who reads the warnings. 💀

• -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.

okay that's the whole thing, you ate, go assemble something gorgeous ✨🧚💜

this page was brought to you by velvetg_63 version 1.2.10+dfsg1, dated July 2018 — mwah, ily, bye 💖🎀🫶