Section | Tool | Purpose |
---|---|---|
Single nucleotide Polymorphisms | InterSnp | Call SNPs between two or more samples |
 | Pebbles | Impute genotypes in output from InterSnp |
 | HapHunt | Phase haplotypes with K-means |
Copy number Variants | GapFall | Identify deletions between two samples |
 | Elfen | Identify covered regions |
 | HMMph | Call copy number variants with HMM |
Bisulfite-sequence Analysis | MetHead | Summarize base pair methylation in bisulfite-sequence data |
GeneVisitor | Bam2Consensus | Generate consensus sequences from one or more samples |
 | Bam2Fastq | Extract mapped and unmapped reads from BAM files |
 | Counter | Summarize read coverage of sequences or regions |
 | SubBam | Extract subset of mapped reads |
Allopolyploid analysis | PolyCat | Categorize reads by genome based on similarity to parents |
Scripts | Various | Various |