$ shpc show -f velvet # can SHPC locate the new recipe? yes!
quay.io/biocontainers/velvet
$ shpc install quay.io/biocontainers/velvet:1.2.10--h5bf99c6_4 # installing Velvet
singularity pull --name /software/projectcode/rsrchr/shpc/containers/quay.io/biocontainers/velvet/1.2.10--h5bf99c6_4/quay.io-biocontainers-velvet-1.2.10--h5bf99c6_4-sha256:7fc2606a1431883dcd0acf830abcfeddb975677733d110a085da0f07782f5a27.sif docker://quay.io/biocontainers/velvet@sha256:7fc2606a1431883dcd0acf830abcfeddb975677733d110a085da0f07782f5a27
INFO: Converting OCI blobs to SIF format
INFO: Starting build...
Getting image source signatures
[..]
INFO: Creating SIF file...
/software/projects/projectcode/rsrchr/shpc/containers/quay.io/biocontainers/velvet/1.2.10--h5bf99c6_4/quay.io-biocontainers-velvet-1.2.10--h5bf99c6_4-sha256:7fc2606a1431883dcd0acf830abcfeddb975677733d110a085da0f07782f5a27.sif
Module quay.io/biocontainers/velvet:1.2.10--h5bf99c6_4 was created.
$ module load quay.io/biocontainers/velvet/1.2.10--h5bf99c6_4/module # loading module
$ velvetg --help # testing a command
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 |