Quickstart

GRAFIMO usage options

To check out all usage instructions available for GRAFIMO type

grafimo --help  # or grafimo -h

GRAFIMO VG scan

Scannig a genome variation graph (built constructing graph for each chromosome) for the occurrences of a DNA motif in a set of genomic regions defined in a BED file. Note that all VG must have the XG and GBWT indexes stored in the same location. Note that the motif(s) can be given in MEME or JASPAR format.

grafimo -d /path/to/directory/storing/my/graphs/ -b /path/to/my/bedfile -m path/to/my/motif

Scanning a whole genome graph for the occurrences of a DNA motif in a set of genomic regions defined in a BED file. Note that the whole genome VG must have the XG and GBWT indexes stored in the same location. Note that the motif(s) can be given in MEME or JASPAR format.

grafimo -g /path/to/my/whole/genome/vg -b /path/to/my/bedfile -m /path/to/my/motif

GRAFIMO VG build

Building the genome variation graph with GRAFIMO (GRAFIMO will build a graph for each single chromosome). Note that the names of chromosomes must be identical on both the reference genome and the VCF file containing the genomic variants; for example if in the VCF the chromosome 1 is named as 1, the reference genome FASTA file must contain >1 instead of >chr1 in chromosome 1 sequence header.

grafimo buildvg -l /path/to/reference/genome -v /path/to/vcf/file 

Running examples

Running examples are available in tutorials directory. In each tutorial are described the main functionalities of GRAFIMO.