A complete pipeline for metagenomic analysis
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Updated
Nov 15, 2024 - C
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metagenomes
Here are 38 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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Nov 28, 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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Nov 27, 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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Nov 5, 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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Oct 25, 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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Updated
Oct 25, 2024
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