40 Open source projects that are alternatives of or similar to charcoal

ganon classifies short DNA sequences against large sets of genomic sequences efficiently, with download and update of references (RefSeq/Genbank), taxonomic (NCBI/GTDB) and hierarchical classification, customized reporting and more

Bonsai: Fast, flexible taxonomic analysis and classification

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.

From genomes to phenotypes: Traitar, the microbial trait analyzer

Fast in-silico normalization algorithm for NGS data

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

MaAsLin2: Microbiome Multivariate Association with Linear Models

A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.

An interactive radial tree for functional hierarchies and omics data visualization

Metagenomics calibration R package

micca - MICrobial Community Analysis

No description or website provided.

VirNet: A deep attention model for viral reads identification

R package for microbiome biomarker discovery

GraphBin: Refined binning of metagenomic contigs using assembly graphs

Mapping-Assisted Targeted-Assembly for Metagenomics

Compare different differential abundance and expression methods

A package for designing compact and comprehensive capture probe sets.

Improving genome bins through the combination of different binning programs

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

🚀 A sequencing simulator

AMBER: Assessment of Metagenome BinnERs

The MG-RAST Backend -- the API server

Predict AMPs in (meta)genomes and peptides

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

Deep learning for Metagenome Assembly Error Detection

A robust, extensible metagenomics pipeline

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

Meta-Omics Software for Community Analysis

gargammel is an ancient DNA simulator

Strain-level abundances estimation in metagenomic samples using variation graphs

No description or website provided.

Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

Toolkit for k-mer with taxonomic information

Learn interpretable computational phenotyping models from k-merized genomic data

interactive Multi Objective K-mer Analysis

A compressed, associative, exact, and weighted dictionary for k-mers.

This work presents a way to write extensions in Rust and use them in Python, using sourmash as an example.