Installation:
conda install -c bioconda vulcan
program usage:
usage: vulcan [-h] -i INPUT [INPUT ...] -r REFERENCE -o OUTPUT [-w WORK_DIR] [-t THREADS] [-p PERCENTILE [PERCENTILE ...]] [-f] [-d] [-R] [-clr | -hifi | -ont | -any | -hclr | -hhifi | -hont | -cmd]
vulcan: map long reads and prosper🖖, a long read mapping pipeline that melds minimap2 and NGMLR
optional arguments:
-h, --help show this help message and exit
-w WORK_DIR, --work_dir WORK_DIR
Directory of work, store temp files, default: ./vulcan_work
-t THREADS, --threads THREADS
threads, default: 1
-p PERCENTILE [PERCENTILE ...], --percentile PERCENTILE [PERCENTILE ...]
percentile of cut-off, default: 90
-f, --full keep all temp file
-d, --dry only generate config
-R, --raw_edit_distance
Use raw edit distance to do the cut-off
-clr, --pacbio_clr Input reads is pacbio CLR reads
-hifi, --pacbio_hifi Input reads is pacbio hifi reads
-ont, --nanopore Input reads is Nanopore reads
-any, --anylongread Don't know which kind of long read
-hclr, --humanclr Human pacbio CLR read
-hhifi, --humanhifi Human pacbio hifi reads
-hont, --humannanopore
Human Nanopore reads
-cmd, --custom_cmd Use minimap2 and NGMLR with user's own parameter setting
Required arguments::
-i INPUT [INPUT ...], --input INPUT [INPUT ...]
input read path, can accept multiple files
-r REFERENCE, --reference REFERENCE
reference path
-o OUTPUT, --output OUTPUT
vulcan's output's prefix, the output will be prefix_{percentile}.bam
example:
./vulcan -r ./test/GCF_000146045.2_R64_genomic.fna -i ./test/test_reads.fa -w ./test/ -o vulcan