Software tools

Flye (ABruijn)

    A de novo assembler of long error-prone reads using repeat graphs.



GraphBin

    A binning tool for metagenomic contigs using assembly graphs.



GraphBin2

    A new generation of GraphBin that supports overlapped binning of metagenomic contigs.



MetaBCC-LR

    Metagenomics binning by coverage and composition for long reads.


PlasLR

    Adaptation of contig based plasmid classification for error prone long reads to improved genome assembly.



MultiTrans

    Reconstruct transcripts through a mixed integer linear programming on assembly or splicing graphs.


DCHap

    A divide-and-conquer haplotype phasing algorithm for third-generation sequencing data.


Kmer2SNP

    A reference-free and alignment-free variants calling tool for next-generation sequencing data.


BaterialMS

    Bacterial whole cell typing by mass spectra with bootstrapping assessment.


BacteriaMS-mixture

    Bacterial mixture identification using MALDI-TOF mass spectrometry.


MLGO

    Phylogeny reconstruction and ancestral inference from gene-order data.


TIBA

    Phylogeny inference from rearrangement data with bootstrap analysis.


MatchingDistance

    A distance measure for phylogenetic trees based on matching.


DyHATR

    A dynamic heterogeneous representation learning method used for temporal link prediction.