Command Line

Usage

Run snipgenie for the cli or snipgenie-gui for the desktop version. You require a reference genome and reads in fastq format at minimum as input.

Command line options

This will run the entire process based on a set of options given at the terminal::

  -h, --help            show this help message and exit
  -i FILE, --input FILE
                        input folder(s)
  -M FILE, --manifest FILE
                        manifest file with samples, optional - overrides input
  -r FILE, --reference FILE
                        reference genome filename
  -S SPECIES, --species SPECIES
                        set the species reference genome, overrides -r. possible values are
                         Mbovis-AF212297, MTB-H37Rv, MAP-K10, M.smegmatis-
                        MC2155, Mycoplasmabovis-PG45, Sars-Cov-2
  -g FILE, --genbank_file FILE
                        annotation file, optional
  -t THREADS, --threads THREADS
                        cpu threads to use
  -sep LABELSEP, --labelsep LABELSEP
                        symbol to split the sample labels on if parsing filenames
  -x LABELINDEX, --labelindex LABELINDEX
                        position to extract label in split filenames
  -w, --overwrite       overwrite intermediate files
  -U, --unmapped        whether to save unmapped reads
  -Q QUALITY, --quality QUALITY
                        right trim quality, default 25
  -f FILTERS, --filters FILTERS
                        variant calling post-filters
  -m MASK, --mask MASK  supply mask regions from a bed file
  -pf PROXIMITY, --proximity PROXIMITY
                        proximity filter value, set 0 to not apply filter
  -u, --uninformative   keep uninformative sites when calling variants
  -p PLATFORM, --platform PLATFORM
                        sequencing platform, change to ont if using oxford nanopore
  -a ALIGNER, --aligner ALIGNER
                        aligner to use, bwa, subread, bowtie or minimap2
  -b, --buildtree       whether to build a phylogenetic tree, requires RaXML
  -N BOOTSTRAPS, --bootstraps BOOTSTRAPS
                        number of bootstraps to build tree
  -o FILE, --outdir FILE
                        Results folder
  -old, --old_method    use old calling method
  -q, --qc              QC report
  -s, --stats           Calculate read length and mapping stats
  -d, --dummy           Check samples but don't run
  -T, --test            Test run
  -v, --version         Get version

Examples

Call with your own reference fasta file:

snipgenie -r reference.fa -i data_files -o results

Use an in built species genome as reference. This will also supply an annotation file. The current options are Mbovis-AF212297, MTB-H37Rv, MAP-K10, M.smegmatis-MC2155:

snipgenie -S Mbovis-AF212297 -i data_files -o results

Provide more than one folder:

snipgenie -r reference.fa -i data_files1 -i data_files2 -o results

Provide an annotation (genbank format) for consequence calling:

snipgenie -r reference.fa -g reference.gb -i data_files -o results

Add your own filters and provide threads:

snipgenie -r reference.fa -i data_files -t 8 -o results` \
 -f 'QUAL>=40 && INFO/DP>=20 && MQ>40'