VELVETG_63_LONG(1)

💖 VELVETG_63_LONG(1) 💖

User Commands — velvetg_63_long

okay bestie, welcome to the manual page for velvetg_63_long, aka de Bruijn graph construction, error removal and repeat resolution — but like, the MAXKMERLENGTH = 63, LONGSEQUENCES flavor. this is the one that eats long reads for breakfast and still shows up to class. 🦋

✨ NAME ✨

velvetg_63_long — de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 63, LONGSEQUENCES)

🌸 DESCRIPTION 🌸

the whole vibe, in one line:

Usage: ./velvetg directory [options]

directory : the working directory name. that's where everything lives, bestie.

🎀 Standard options 🎀

the classics. the staples. the everyday fits. 💅

• -cov_cutoff <floating-point|auto> — removes low coverage nodes AFTER tour bus, or lets 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 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 ✨extra✨. these are the ones you read twice, iykyk.

• -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)

📌 [replace '*' by nothing, '2' or '_long' as necessary]

• -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 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, bestie, it's gone gone) (default: no)
• -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 👑

what you get at the end. the ~reveal~. 🎁

• 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, no cap. go assemble something iconic. 🧚💜

velvetg_63_long 1.2.10+dfsg1 — July 2018 🎀 slay, bye bestie!! 🌈✨