Projects in Awesome Lists tagged with metagenomes

https://github.com/althonos/pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

bioconda bioinformatics cython-wrapper gene-finding genome metagenomes orf-finder prodigal python python-interface python-library simd

Last synced: 08 Apr 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: 16 Dec 2024

https://github.com/muellan/metacache

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

bioinformatics bioinformatics-algorithms bioinformatics-tool classification dna-sequences fasta fastq genome genomic-data-analysis long-reads metagenomes metagenomic-analysis metagenomic-classification metagenomic-data metagenomics ncbi-refseq read-mapping refseq short-read-mapper taxonomy

Last synced: 09 Apr 2025

https://github.com/mtisza1/Cenote-Taker2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)

annotation cenote-taker2 cenote-unlimited-breadsticks discovery genbank hallmark hhblits hhsearch metagenomes prophage prophage-prediction virome virus virus-discovery virus-evolution virus-sequences

Last synced: 23 Mar 2025

https://github.com/cafferychen777/microbiomestat

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

16s-rrna amplicon-sequencing dada2 longitudinal-data metagenomes metagenomic-analysis microbiome microbiome-analysis microbiome-data microbiome-workflow omics omics-data-integration phyloseq qiime2 statistics visualization

Last synced: 16 Apr 2025

https://github.com/samstudio8/gretel

An algorithm for recovering haplotypes from metagenomes

bioinformatics haplotypes metagenomes

Last synced: 28 Feb 2025

https://github.com/althonos/pyskani

PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.

ani average-nucleotide-identity bioinformatics metagenomes python-bindings python-library taxonomy

Last synced: 02 Jan 2025

https://github.com/althonos/pyfastani

Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.

ani average-nucleotide-identity bioinformatics cython-library metagenomes python-bindings python-library taxonomy

Last synced: 20 Mar 2025

https://github.com/linsalrob/partie

PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied annotations of the data sets can not be trusted, and so PARTIE allows automatic separation of the data.

bioinformatics metagenomes metagenomic-data metagenomics sra

Last synced: 23 Mar 2025

https://github.com/cafferychen777/microbiomestat-turtorial-professional-version

MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.

16s 16s-rrna 16s-seq analysis data-analysis metagenomes metagenomic-analysis metagenomic-pipeline metagenomics microbiome microbiome-analysis microbiome-analysis-pipelines microbiome-data microbiome-workflow omics omics-data omics-data-analysis omics-data-integration visualization

Last synced: 16 Mar 2025

https://github.com/cmungall/gold-ontology

environment-ontology gold-classification jgi metagenomes

Last synced: 17 Mar 2025

https://github.com/gauravcodepro/pangenomes-metagenomes

a workflow for complete analysis of bacterial metagenomes and pagenome graphs and direct viewing in panchae. It will also analyze metagenomes from both illumina and long reads

bacterial-genomes bioinformatics metagenomes metagenomics-data pangenomics pangraphs