https://github.com/tseemann/abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

antimicrobial-resistance-genes bioinformatics-tool contigs genomic-regions virulence-genes

Last synced: 12 Apr 2025

https://github.com/gabaldonlab/redundans

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

assembled-contigs assembly bioinformatics closing contigs docker-image fasta gap genome-assembly genomics heterozygous mate-pairs paired-end pipeline polymorphic python scaffolding

Last synced: 20 Aug 2025

https://github.com/oschwengers/platon

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

assembly bacteria bioinformatics contigs microbiology ngs plasmids wgs

Last synced: 12 Aug 2025

https://github.com/mcveanlab/mccortex

De novo genome assembly and multisample variant calling

contigs cortex de-bruijn-graphs genome-analysis genome-assembly genome-graph genomics kmer variant-calling

Last synced: 17 Dec 2025

https://github.com/smaegol/plasflow

Software for prediction of plasmid sequences in metagenomic assemblies

classification contigs fasta metagenome metagenome-assembly metagenomes plasflow plasmid plasmid-sequences plasmids prediction tensorflow

Last synced: 21 Jul 2025

https://github.com/tobiasrausch/wally

Wally: Visualization of aligned sequencing reads and contigs

alignment assembly contigs genomics mapping plotting sequencing sequencing-data visualization

Last synced: 13 Apr 2025

https://github.com/tanghaibao/allhic

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

contigs genetic-algorithm genome-assembly genome-scaffolding genomics golang heterozygous hi-c inter-contig-links lachesis pipeline polyploid

Last synced: 09 Apr 2025

https://github.com/metagentools/gbintk

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

assembly-graph bioinformatics contigs metagenomic-binning metagenomics

Last synced: 25 Dec 2025

https://github.com/haradama/plasmidpicker

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

bioinformatics classification contigs fasta logistic-regression metagenome metagenomics minhash plasmids

Last synced: 13 Apr 2025

https://github.com/haradama/phash

Software to identify known plasmid sequence from metagenomic assembly using Minhash

bioinformatics biology contigs fasta golang metagenome metagenomics minhash plasmid plasmids

Last synced: 05 Mar 2025

https://github.com/zyxue/vr2c

Visualize read-to-contig alignment during assembly analysis

alignment contig-coverage contigs genome-assembly read-to-contig-alignment transcriptome-assembly

Last synced: 30 Mar 2025

https://github.com/schultzm/pandoo

assemblies contigs isolate pipeline ruffus short-read tree

Last synced: 10 Apr 2025