Sergio Pulido-Tamayo, Aminael Sánchez-Rodríguez, Toon Swings, Bram Van den Bergh, Akanksha Dubey, Hans Steenackers, Jan Michiels, Jan Fostier, Kathleen Marchal
EVORhA (EVOlutionary Reconstruction of hAplotypes), a haplotype reconstruction method that can handle haplotype reconstruction also in slowly evolving species.
DownloadExample: java -jar EVORhA.jar completeAnalysis example/EcoliK12MG1655_truncated.fasta example/file_sorted.bam
Usage: java -jar EVORhA.jar <method> <files> Methods: - snpCounter: Count SNPs in sorted bam file files: <genotype fasta> <annotation gff> <sorted bam> <outputfile snpout> - subsMatrixBuilder: build a substitution matrix from observed data files: <snp count snpout> <outputfile blosum> - windowFinder: find and order a list of windows files: <snp count snpout> <outputfile windows> - windowProcessor: process each window in window file files: <genotype fasta> <sorted bam> <bam index bam.bai> <snp count snpout> <window list windows> <sub matrix blosum> <output sampling file> - windowExtention: load processing results and extend window haplotypes files: <genotype fasta> <snp count snpout> <sub matrix blosum> <process file> <output haplotype fasta file - globalReconstruction: load extension results and construct haplotypes files: <genotype fasta> <snp count snpout> <sub matrix blosum> <extension file> <output haplotype fasta file - joinGlobalHap2fasta: join different global.hapfreq files into one joined hap files with fasta format files: <genotype fasta> <file1.global.hapfreq> <file2.global.hapfreq> ... <fileN.global.hapfreq> <output.join.fasta file> - completeAnalysis: run the complete pipeline to a bam file files: <genotypeName - .fasta & .gff> <sorted bam> - evolutionExperiment: analize different timepoint of an evolution experiment files: <genotype fasta> <baseNameTimePoint1> <baseNameTimePoint2> ... <baseNameTimePointN> <joinFile> NOTE: if only one file is used its assumed all files have the same name e.g. "HaplotypeReconstruction snpCounter REL606" is the same as "HaplotypeReconstruction snpCounter REL606_sorted.bam REL606.fa REL606.gff REL606.snpout"
Reporting bugs or asking for features are much welcome!
Please contact us via email at sergio.pulidotamayo[[@]]ugent.be