contigs

tseemann/abricate

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

Gabaldonlab/redundans

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

oschwengers/platon

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

tobiasrausch/wally

Wally: Visualization of aligned sequencing reads and contigs

mcveanlab/mccortex

De novo genome assembly and multisample variant calling

COMBINE-lab/pufferfish

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

smaegol/PlasFlow

Software for prediction of plasmid sequences in metagenomic assemblies

metagentools/GraphBin

✨🧬 Refined binning of metagenomic contigs using assembly graphs

nf-core/funcscan

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

metagentools/MetaCoAG

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

tanghaibao/allhic

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

morispi/CONSENT

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

metagentools/GraphBin2

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

merenlab/reads-for-assembly

Simulate metagenomic short reads from one or more populations.

raymondkiu/bioinformatics-tools

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

metagentools/gbintk

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

LeonDlugosch/MetaSeq-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.

haradama/PlasmidPicker

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

mtisza1/Cenote_Unlimited_Breadsticks

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

masikol/barapost

Toolkit for binning FASTA, FASTQ and FAST5 files according to taxonomic annotation

algbio/Introduction-to-Applied-Bioinformatics

Genome assembly - From theory to practice (and back)

CNuge/snp-placer

Take information about snps on short sequence reads and accurately place the snps in a reference genome

DaniRuizPerez/SeniorProjectChromevol

BSc Senior Project, Bioinformatics Django web platform for storage and analysis of Biological data. Still in use by the group CHROMEVOL from FIU

haradama/pHash

Software to identify known plasmid sequence from metagenomic assembly using Minhash

lisavader/plasmidEC

An ensemble of plasmid classification tools

quxiaojian/get_cp_and_mt_genes_from_contigs_of_genome-skimming_or_transcriptome_data

get chloroplast and mitochondrial genes from contigs of genome-skimming or transcriptome data

AntoineHo/CASH

Compare and shuffle heterozygosity using BED and VCF files

zyxue/vr2c

Visualize read-to-contig alignment during assembly analysis

cpolano/phytoassembly

Sequencing of unculturable plant pathogens

erg55/Simon-lab-workshop

Learning!

mansikath/whole-genome-sequencing-pipeline

A comprehensive workflow for de novo assembly of whole-genome shotgun sequencing data using Velvet, followed by BLAST searches to analyze assembled contigs.

NCBI-Codeathons/Domain_HMM_Boundaries

Refining Domain Boundaries and Performing Large Scale Parsing

schultzm/pandoo

annalisaxamin/CMG_project

This project is part of the course of Computational Microbial Genomics, held by Nicola Segata (A.Y. 2021-2022) @ University of Trento.

tmaklin/unmulti

Split a multifasta file into many fasta files containing a single sequence, or extract a list of sequences/contigs. Supports compressed input and output files.