Genome-scale algorithmics (GSA)
Software
Group webpage has moved to a new location: https://www.helsinki.fi/en/researchgroups/genome-scale-algorithmics
- PanVC: A framework to Pan-Genomize your Variant Calling pipeline
- CHICA: CHIC Aligner for enabling scalable read alignment on multiple reference -based pan-genome representations
- MetaFlow: a program for community profiling of a metagenomic sample, described in our RECOMB 2016 paper
- Traphlor: A software for RNA transcript expression prediction from long read RNA-sequencing data. See our BIOINFORMATICS 2016 paper.
- BW4SA library contains some proof-of-concept implementations of the various sequence analysis tasks considered in our ESA 2013 paper.
- Maximal Unique Matches computed with a bidirectional BWT index in SDSL libary following our ESA 2013 paper.
- Traph. A software for RNA transcript expression prediction from RNA-sequencing data. See our RECOMB-seq and WABI 2013 papers.
- DAlign Computes the unit cost edit distance between a haploid and a reference guided recombination of two diploids.
- Normalized N50 calculator. A tool to extract correctly aligning parts of (scaffold) assemblies and compute the resulting normalized N50. After publishing we noticed that GAGE also has similar tool to compute corrected N50. The strategy to extract correct alignments is different in these two, but on real data they seem to obtain similar results.
- geneneralized compressed suffix array for indexing multiple alignment of several reference genomes or reference genome plus known variants.
- all-against-all suffix/prefix alignment for creating overlap graphs for de novo fragment assembly from short reads. Allows approximate overlaps and works in small space.
- readaligner for mapping (short) DNA reads into reference sequences. This is not as fast as some other Burrows-Wheeler-based aligners, but implements faithfully k-mismatches and k-errors search where some other tools may solve a slighly different or implicitly defined problem.
- See the listing at SuDS group for earlier implementations.