Population genomics from metagenomes
POGENOM takes as input a file of the variant call format (VCF). This is generated by mapping one or several metagenome samples against a reference genome with a read aligner and calling variants using a variant caller. POGENOM calculates the nucleotide diversity (𝛑) within each sample. If a multiple-sample vcf file is provided as input, the fixation index (FST) will also be calculated between each pair of samples. If, in addition to the VCF file, an annotation file of the General Feature Format (GFF) is provided as input, gene-wise 𝛑 and FST will also be calculated. If, further, a genetic code file is provided, gene-wise 𝛑 and FST will be calculated also at the amino acid level. Now also non-synonymous to synonymous polymorphism rates (pN/pS) will be calculated for each gene in each sample. POGENOM also calculates some of the above parameters for all samples collectively, treating them as a metasample. For gene- and loci-wise calculations, a genome sequence needs to be provided. This can either be included in the end of the GFF file (in fasta version) or be provided as a separate fasta file.
Download the latest POGENOM distribution from https://github.com/EnvGen/POGENOM/releases and extract the files. You need to have Perl installed on your computer to run POGENOM. When running POGENOM, either move to the directory where you have put the files or give the path to the files when running, i.e. perl path/to/pogenom.pl ...
Either:
perl pogenom.pl --vcf_file VCF_FILE --out OUTPUT_FILES_PREFIX --genome_size GENOME_SIZE [--help]
Or:
perl pogenom.pl -vcf_file VCF_FILE --out OUTPUT_FILES_PREFIX --gff_file GFF_FILE [--help]
Or:
perl pogenom.pl -vcf_file VCF_FILE --out OUTPUT_FILES_PREFIX --fasta_file FASTA_FILE [--help]
--vcf_file VCF_FILE Specify vcf file with data from a single or multiple samples.
--out OUTPUT_FILES_PREFIX Specify the prefix of the output file name(s) (overwrites existing files with same names).
--genome_size GENOME_SIZE Specify genome size (in bp; integer). Not required if --gff_file or --fasta_file with genome sequence is given.
--gff_file GFF_FILE Specify gff file. Either this, --genome_size or --fasta_file must be given.
--fasta_file FASTA_FILE Specify fasta file. Either this, --genome_size or --gff_file must be given
--genetic_code_file GENETIC_CODE_FILE Specify genetic code file. E.g. standard_genetic_code.txt in the POGENOM distribution.
--loci_file LOCI_FILE Specify file with ids of loci to include.
--min_count MIN_COUNT Specify minimum coverage for a locus to be included for the sample.
--min_found MIN_FOUND_IN Specify minimum number samples that a locus needs to be present in to be included.
--subsample SUBSAMPLE Specify coverage level at which to subsample.
--keep_haplotypes If this is used, POGENOM will not split haplotypes into single-nucleotide variants, which is otherwise the default behaviour.
--vcf_format Specify VCF file format version. Can be set to freebayes (default) or GATK.
--help To print help message on screen.
POGENOM doesn't have a paper yet, meanwhile please cite it like this:
Andersson AF, Sjöqvist C (2017). POGENOM: population genomics from metagenomes. https://github.com/EnvGen/POGENOM.