A complete pipeline for metagenomic analysis
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Dec 3, 2024 - C
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metagenomes
Here are 36 public repositories matching this topic...
Assembly and binning of metagenomes
workflow bioinformatics nanopore pipeline annotation nextflow assembly metagenomics binning metagenomes nanopore-sequencing nf-core long-read-sequencing
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Dec 13, 2024 - Nextflow
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
python bioinformatics genome python-library simd bioconda python-interface metagenomes cython-wrapper prodigal gene-finding orf-finder
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Nov 12, 2024 - Cython
Software for prediction of plasmid sequences in metagenomic assemblies
tensorflow prediction classification fasta plasmid metagenomes contigs metagenome plasmid-sequences metagenome-assembly plasmids plasflow
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Jun 28, 2021 - Python
This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
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Apr 22, 2021 - Python
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
bioinformatics genome taxonomy metagenomics classification fasta fastq metagenomes dna-sequences short-read-mapper read-mapping metagenomic-analysis metagenomic-classification genomic-data-analysis bioinformatics-algorithms long-reads metagenomic-data refseq ncbi-refseq bioinformatics-tool
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Oct 1, 2024 - C++
Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)
virus annotation discovery genbank hhblits hhsearch metagenomes virome virus-discovery prophage hallmark virus-evolution cenote-taker2 prophage-prediction virus-sequences cenote-unlimited-breadsticks
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Jan 19, 2024 - Shell
Minimum Information about any (X) Sequence” (MIxS) specification
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Dec 4, 2024 - Python
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
visualization statistics longitudinal-data microbiome omics metagenomes metagenomic-analysis microbiome-analysis phyloseq dada2 omics-data-integration amplicon-sequencing microbiome-data qiime2 16s-rrna microbiome-workflow
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Nov 24, 2024 - R
An algorithm for recovering haplotypes from metagenomes
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Jun 29, 2021 - Python
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.
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Feb 25, 2023 - Perl
PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
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Dec 6, 2024 - Rust
Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
bioinformatics taxonomy python-library python-bindings metagenomes cython-library ani average-nucleotide-identity
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Dec 5, 2024 - Cython
This is the codebase for Faucet, described in our manuscript: https://academic.oup.com/bioinformatics/article/34/1/147/4004871, by Roye Rozov, Gil Goldshlager, Eran Halperin, and Ron Shamir
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May 21, 2017 - C++
MetaCarvel: A scaffolder for metagenomes
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Sep 17, 2024 - C++
Raw sequence metagenomic reads pre-processing: trimming, QC, and host contamination
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Jul 24, 2024 - Python
FOCUS: An Agile Profiler for Metagenomic Data
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Sep 15, 2024 - Python
A few scripts to help with the installation of MetaErg, the contig/bin annotation pipeline
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Feb 13, 2020 - Shell
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.
visualization analysis metagenomics data-analysis microbiome omics 16s metagenomes metagenomic-analysis microbiome-analysis omics-data-integration microbiome-data 16s-rrna microbiome-workflow metagenomic-pipeline omics-data microbiome-analysis-pipelines 16s-seq omics-data-analysis
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Oct 25, 2024
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