---
name: "velvetg_long"
section: "1"
platform: "linux"
package: "velvet-long"
version: "1.2.10+dfsg1-9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/velvetg_long"
---

# velvetg\_long(1)

de Bruijn graph construction, error removal and repeat resolution (LONGSEQUENCES)

## NAME

velvetg\_long - de Bruijn graph construction, error removal and repeat resolution (LONGSEQUENCES)

## DESCRIPTION

Usage: ./velvetg directory \[options\]

- directory

  : working directory name

### Standard options:

- **-cov\_cutoff** \<floating-point\|auto\>

  : removal of low coverage nodes AFTER tour bus or allow the system to infer it

-

  (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 contigs.fa file (default: hash length \* 2)

- **-amos\_file** \<yes\|no\>

  : export assembly to AMOS file (default: no export)

- **-exp\_cov** \<floating point\|auto\>

  : expected coverage of unique regions or allow the system to 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:

- **-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 respective dataset (default: 10% of corresponding length)

-

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

- **-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 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 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)

- **-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