Genome assembly evaluation tool

🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

De novo genome assembly and multisample variant calling

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

An efficient index for the colored, compacted, de Bruijn graph

Wally: Visualization of aligned sequencing reads and contigs

Software for prediction of plasmid sequences in metagenomic assemblies

✨🧬 Refined binning of metagenomic contigs using assembly graphs

(Meta-)genome screening for functional and natural product gene sequences

Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

Scalable long read self-correction and assembly polishing with multiple sequence alignment

☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs

Simulate metagenomic short reads from one or more populations.

Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files

🌟🧬 GraphBin-Tk: assembly graph-based metagenomic binning toolkit

This pipeline is intended to be a convenient way to work though large sets of metagenomic or metatranscriptiomic datasets while also retaining high analytical flexibility due to retained intermediate results that might be useful outside of the intended purpose.

Software to identify plasmid sequence data from metagenome using logistic regression and Minhash

DEPRECATED: Discover divergent virus sequences, prune flanking cellular sequences, make basic report