The research activities of PANGAIA involve the development of innovative software. In this page you can find the list.

Please do not hesitate to contact us if you find any error, if you want to suggest improvements, or if you want to contribute.

Osprey

Link: https://github.com/fmfi-compbio/osprey/
License: Apache-2.0
Description: Real-time high accuracy CPU basecaller for Oxford nanopore reads.

Heron

Link: https://github.com/fmfi-compbio/heron/
License: Apache-2.0
Description: High accuracy GPU basecaller for Oxford nanopore reads.

plASgraph

Link: https://github.com/cchauve/plASgraph/
License: BSD-3-Clause
Description: Plasmid contig detection in bacterial assembly graphs.

MCDP

Link: https://github.com/fmfi-compbio/mc-overlaps/
License: MIT
Description: Significance computation for genome annotation overlap.

DeepNano-coral

Link: https://github.com/fmfi-compbio/coral-basecaller/
License:
Description: Fast and energy-efficient basecaller for Oxford nanopore reads running on Coral edge TPU device.

shark

Link: https://algolab.github.io/shark/
License: GPL-3.0
Description: Fast tool for mapping-free gene separation of reads, using Bloom filter.

PHERI

Link: https://github.com/andynet/pheri
License: MIT
Description: Phage Host ExploRatIon tool. The main purpose of this program is to predict phage hosts from sequence in FASTA format. Currently it is able to predict 8 host genera with very high accuracy (around 97%) – Arthrobacter, Escherichia, Gordonia, Lactococcus, Mycobacterium, Pseudomonas, Staphylococcus, Streptococcus.

IUPACpal

Link: https://sourceforge.net/projects/iupacpal/
License: GPL
Description: An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. IUPACpal is an exact tool for efficient identification of inverted repeats in IUPAC-encoded DNA sequences as substrings of a large text, allowing also for potential mismatches and gaps.

Strainline

Link: https://github.com/HaploKit/Strainline/
License: GPL-3.0
Description: Full-length de novo viral haplotype reconstruction from noisy long reads.

phasebook

Link: https://github.com/phasebook/phasebook/
License: GPL-3.0
Description: Haplotype-aware de novo assembly of diploid genomes from long reads.

PLAST

Link: https://gitlab.ub.uni-bielefeld.de/gi/plast/
License: GPL-3.0
Description: Pangenome Local Alignment Search Tool.

rust-mdbg

Link: https://github.com/ekimb/rust-mdbg/
License: MIT
Description: Minimizer-space de Bruijn graphs (mdBG) for whole-genome assembly.

deepnano-blitz

Link: https://github.com/fmfi-compbio/deepnano-blitz/
License: MIT
Description: Ultra fast ONT basecaller.

mp3

Link: https://github.com/AlgoLab/mp3treesim/
License: MIT
Description: Triplet-based similarity score for fully multi-labeled trees with poly-occurring labels.

PingPong

Link: https://github.com/parsoa/pingpong/
License: MIT
Description: Sample-specific string detection from accurate long reads.

corer

Link: https://gitlab.ub.uni-bielefeld.de/gi/corer/
License: GPL-3.0
Description: Sequence-based Pangenomic Core Detection.

MALVIRUS

Link: https://github.com/algolab/malvirus/
License: GPL-3.0
Description: Fast and accurate tool for genotyping haploid individuals.

MetaBooster/HiFiBooster

Link: https://github.com/HaploKit/metagenome-asm/
License: GPL-3.0
Description: Strain aware metagenome assembly from PacBio CLR and ONT sequencing data.