In here you can find tools created by the team members and students, but also some tools created by other people which we use on regular basis.


Our tools:

 Useful other people's tools:

  • BBMap - A DNA and RNA mapping tool adapted to work with third generation sequencing technologies
  • Gepard - Genome pair rapid dotter
  • IGV - Interactive genomics viewer
  • MiniMap2 - Versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database
  • Hifiasm - Fast haplotype-resolved de novo assembler initially designed for PacBio HiFi reads
  • Shasta - De novo assembler for long reads, optimized for Oxford Nanopore (ONT) reads
  • Verkko -  Hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads
  • Flye - De novo assembler for single-molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies
  • GfaViz -  Graphical interactive tool for the visualization of sequence graphs in GFA format
  • Bandage -  Program for visualising de novo assembly graphs
  • D-Genies - A standalone and WEB application performing large genome alignments using minimap2 software package and generating interactive dot plots
  • Minigraph - Sequence-to-graph mapper and graph constructor
  • GraphAligner - Seed-and-extend program for aligning long error-prone reads to genome graphs
  • Samba - Genome assembly and analysis toolkit contains of MaSuRCA genome assembler, QuORUM error corrector for Illumina data, POLCA genome polishing software, Chromosome scaffolder, jellyfish mer counter, and MUMmer aligner
  • DeepVariant -  Analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
  • Yak - Tool that robustly estimates the base accuracy of CCS reads and assembly contigs and investigates the systematic error rate of CCS reads
  • Quast  - Genome assembly evaluator
  • Busco - Tool that uses various evolutionary information and gives us a measure that tells us how well a given genome assembled is