Create statistic summary of an Oxford Nanopore read dataset

Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and short reads (hybrid strategy)

LongQC is a tool for the data quality control of the PacBio and ONT long reads.

LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB.

Classifier for metagenomic sequences using FM-index with run-block compressed BWT.

Metagenomic classification of long-read sequencing data

The second version of the Kraken taxonomic sequence classification system

A versatile pairwise aligner for genomic and spliced nucleotide sequences

A fast and sensitive gapped read aligner

Assembly and binning of metagenomes

quality filtering tool for long reads

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

post processing of bacterial pangenome gene presence/absence matrices

Recombination-free trees

A microbial genomic analysis pipeline used by the Djordjevic Lab

SRA Tools

Bioinformatics tool to find integrons in bacterial genomes

🎄Visualization and annotation of phylogenetic trees

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org

Cutadapt removes adapter sequences from sequencing reads

Read trimming tool for Illumina NGS data.

Official git repository for Biopython (originally converted from CVS)

De novo genome assembler for long uncorrected reads

A single molecule sequence assembler for genomes large and small.

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

Ultrafast de novo assembly for long noisy reads (though having no consensus step)