Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
pypi.org "metagenomics" keyword
virstrain 1.17
An RNA/DNA virus strain-level identification tool for short reads.7 versions - Latest release: 2 months ago - 1 dependent repositories - 78 downloads last month - 18 stars on GitHub - 1 maintainer
assnake 0.8.9
System for metagenomics data analysis8 versions - Latest release: about 4 years ago - 1 dependent repositories - 51 downloads last month - 11 stars on GitHub - 1 maintainer
pynteny 0.0.2 removed
Multiple HMM - search via synteny structures in Python1 version - Latest release: over 1 year ago - 20 downloads last month - 5 stars on GitHub
taxpasta 0.6.1
TAXonomic Profile Aggregation and STAndardisation12 versions - Latest release: 7 months ago - 100 downloads last month - 27 stars on GitHub - 6 maintainers
famli 1.2
Functional Analysis of Metagenomes by Likelihood Inferrence3 versions - Latest release: about 4 years ago - 1 dependent repositories - 33 downloads last month - 16 stars on GitHub - 2 maintainers
meteor 2.0.10
Meteor - A plateform for quantitative metagenomic profiling of complex ecosystems11 versions - Latest release: 2 days ago - 1 dependent repositories - 604 downloads last month - 6 stars on GitHub - 2 maintainers
gecco-tool 0.9.10
Gene cluster prediction with Conditional random fields.29 versions - Latest release: 2 months ago - 1 dependent repositories - 283 downloads last month - 52 stars on GitHub - 4 maintainers
metaphlan 4.1.0
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteri...25 versions - Latest release: 3 months ago - 1 dependent repositories - 1.5 thousand downloads last month - 266 stars on GitHub - 2 maintainers
senseppi 0.7.1
SENSE-PPI: Sequence-based EvolutioNary ScalE Protein-Protein Interaction prediction17 versions - Latest release: 23 days ago - 204 downloads last month - 1,259 stars on GitHub - 1 maintainer
strainscan 1.0.14
One efficient and accurate strain-level microbiome composition analysis tool based on reference g...14 versions - Latest release: 7 months ago - 1 dependent repositories - 79 downloads last month - 30 stars on GitHub - 2 maintainers
crocodeel 1.0.3
CroCoDeEL is a tool that detects cross-sample (aka well-to-well) contamination in shotgun metagen...4 versions - Latest release: 5 days ago - 358 downloads last month - 4 stars on GitHub - 2 maintainers
graphbin2 1.2.3
GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs2 versions - Latest release: 19 days ago - 451 downloads last month - 27 stars on GitHub - 2 maintainers
aviary-genome 0.9.0
aviary - metagenomics pipeline using long and short reads20 versions - Latest release: 2 months ago - 122 downloads last month - 67 stars on GitHub - 1 maintainer
deepmased 0.3.1
Deep learning for Metagenome Assembly Error Detection2 versions - Latest release: about 4 years ago - 1 dependent repositories - 24 downloads last month - 25 stars on GitHub - 2 maintainers
phables 1.3.2
Phables: from fragmented assemblies to high-quality bacteriophage genomes21 versions - Latest release: about 2 months ago - 1 dependent repositories - 75 downloads last month - 62 stars on GitHub - 1 maintainer
meta-sparse 0.1.12
SPARSE indexes reference genomes in public databases into hierarchical clusters and uses it to pr...12 versions - Latest release: over 5 years ago - 1 dependent repositories - 39 downloads last month - 17 stars on GitHub - 2 maintainers
recentrifuge 1.14.0
Robust comparative analysis and contamination removal for metagenomics82 versions - Latest release: 3 months ago - 1 dependent repositories - 477 downloads last month - 83 stars on GitHub - 1 maintainer
s3n2bin 0.1.1
Metagenomic binning with semi-supervised siamese neural network2 versions - Latest release: about 3 years ago - 1 dependent repositories - 16 downloads last month - 98 stars on GitHub - 2 maintainers
motu-profiler 3.1.0
Taxonomic profiling of metagenomes from diverse environments with mOTUs33 versions - Latest release: about 1 year ago - 3 dependent repositories - 37 downloads last month - 141 stars on GitHub - 1 maintainer
gtnet 0.1.0
A package for running Genome Taxonomy Network predictions8 versions - Latest release: 2 months ago - 1 dependent repositories - 81 downloads last month - 1 stars on GitHub - 4 maintainers
tiara 1.0.3
A tool for classifying metagenomic data4 versions - Latest release: over 1 year ago - 1 dependent repositories - 111 downloads last month - 44 stars on GitHub - 2 maintainers
semibin 2.1.0
Metagenomic binning with siamese neural networks22 versions - Latest release: 2 months ago - 1 dependent repositories - 94 downloads last month - 96 stars on GitHub - 1 maintainer
dram-bio 1.5.0
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of functio...29 versions - Latest release: 4 months ago - 1 dependent repositories - 413 downloads last month - 223 stars on GitHub - 4 maintainers
chfilter 1.3
Simple instructions to remove 16s rRNA reads from metagenomics samples2 versions - Latest release: about 6 years ago - 1 dependent repositories - 16 downloads last month - 0 stars on GitHub - 2 maintainers
convertfq 0.1.0
convertFQ is used to convert either DNA2RNA or RNA2DNA in a fastq file1 version - Latest release: almost 2 years ago - 13 downloads last month - 0 stars on GitHub - 2 maintainers
microwinebar 0.0.1
MicroWineBar1 version - Latest release: almost 5 years ago - 1 dependent repositories - 14 downloads last month - 4 stars on GitHub - 2 maintainers
mdeepfri 1.1.5
Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.5 versions - Latest release: about 1 month ago - 301 downloads last month - 27 stars on GitHub - 1 maintainer
grabseqs 0.7.0
Easily download reads from next-gen sequencing repositories like NCBI SRA11 versions - Latest release: over 4 years ago - 1 dependent repositories - 86 downloads last month - 101 stars on GitHub - 1 maintainer
drep 3.5.0
De-replication of microbial genomes assembled from multiple samples63 versions - Latest release: 2 months ago - 1 dependent repositories - 545 downloads last month - 234 stars on GitHub - 1 maintainer
mgkit 0.5.8
Metagenomics Framework30 versions - Latest release: over 2 years ago - 2 dependent repositories - 147 downloads last month - 12 stars on GitHub - 2 maintainers
living-tree 0.0.6
An efficient toolkit for constructing and processing taxonomic trees (metagenomic reads count, re...5 versions - Latest release: over 2 years ago - 2 dependent repositories - 48 downloads last month - 4 stars on GitHub - 2 maintainers
prophyle 0.1.0
ProPhyle metagenomic classifier54 versions - Latest release: about 7 years ago - 1 dependent repositories - 918 downloads last month - 31 stars on GitHub - 2 maintainers
mdmcleaner 0.8.7
A pipeline for the assessment, classification and refinement of microbial dark matter SAGs and MAGs5 versions - Latest release: over 1 year ago - 1 dependent repositories - 58 downloads last month - 18 stars on GitHub - 1 maintainer
enrichm 0.6.5
enrichm is a toolbox for comparing the functional composition of population genomes42 versions - Latest release: over 1 year ago - 1 dependent repositories - 161 downloads last month - 78 stars on GitHub - 2 maintainers
superpang 1.3.0
Non-redundant pangenome assemblies from multiple genomes or bins18 versions - Latest release: about 2 months ago - 1 dependent repositories - 25 downloads last month - 11 stars on GitHub - 2 maintainers
microview 0.11.0
Generate reports from metagenomics data12 versions - Latest release: 9 days ago - 184 downloads last month - 0 stars on GitHub - 1 maintainer
signature-snvs 0.0.1
A package to produce signature SNVs for source tracking with methods like FEAST. Given a set of s...1 version - Latest release: over 1 year ago - 19 downloads last month - 2 stars on GitHub - 1 maintainer
microbecensus 1.2.2
A command-line tool for estimating average genome size from shotgun sequence data8 versions - Latest release: 8 months ago - 1 dependent repositories - 43 downloads last month - 37 stars on GitHub - 1 maintainer
genome-uploader 2.1.0
Python script to upload bins and MAGs in fasta format to ENA (European Nucleotide Archive). This ...3 versions - Latest release: 11 days ago - 316 downloads last month - 20 stars on GitHub - 2 maintainers
resmico 1.2.2
Increasing the quality of metagenome-assembled genomes with deep learning18 versions - Latest release: over 1 year ago - 1 dependent repositories - 155 downloads last month - 9 stars on GitHub - 1 maintainer
ocms-16s 0.0.2
OCMS_16S : Oxford Centre for Microbiome Studies pipelines for 16S amplicon sequencing analysis2 versions - Latest release: over 2 years ago - 1 dependent repositories - 9 downloads last month - 2 stars on GitHub - 2 maintainers
randmag 1.2.0
Construct artifical MAGs from complete genomes according to distribution3 versions - Latest release: almost 5 years ago - 1 dependent repositories - 6 downloads last month - 2 maintainers
mglex 0.2.1
MGLEX - MetaGenome Likelihood EXtractor3 versions - Latest release: about 6 years ago - 1 dependent repositories - 13 downloads last month - 6 stars on GitHub - 2 maintainers
Top 9.6% on pypi.org
1 version - Latest release: 9 months ago - 2 dependent repositories - 2 maintainers
metacram 0.5
Comparative Rapid Annotation of Metagenomes1 version - Latest release: 9 months ago - 2 dependent repositories - 2 maintainers
cmash 0.3.0
Fast and accurate set similarity estimation via containment min hash (for genomic datasets).7 versions - Latest release: over 6 years ago - 1 dependent repositories - 60 downloads last month - 42 stars on GitHub - 2 maintainers
strainflair 0.0.2
StrainFLAIR (STRAIN-level proFiLing using vArIation gRaph) is a tool for strain identification an...1 version - Latest release: over 3 years ago - 1 dependent repositories - 7 downloads last month - 24 stars on GitHub - 2 maintainers
mvirs 1.1.1
mVIRs: Localisation of inducible prophages using NGS data1 version - Latest release: about 2 years ago - 1 dependent repositories - 8 downloads last month - 12 stars on GitHub - 2 maintainers
binette 1.0.0
Binette: accurate binning refinement tool to constructs high quality MAGs.3 versions - Latest release: 3 months ago - 24 downloads last month - 1 stars on GitHub - 1 maintainer
nglesspy 0.2.2
NGLessPy: Python interface to NGLess3 versions - Latest release: almost 6 years ago - 1 dependent repositories - 16 downloads last month - 2 stars on GitHub - 2 maintainers
arg-ranker 3.7.2
Ranking the risk of antibiotic resistance for genomes/metagenomes31 versions - Latest release: 4 months ago - 236 downloads last month - 22 stars on GitHub - 1 maintainer
mtags 1.0.4
mTAGs - taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA gene.2 versions - Latest release: over 2 years ago - 1 dependent repositories - 10 downloads last month - 6 stars on GitHub - 2 maintainers
cobra-meta 1.2.3
COBRA (Contig Overlap Based Re-Assembly) is a bioinformatics tool to get higher quality viral gen...4 versions - Latest release: 3 months ago - 59 downloads last month - 37 stars on GitHub - 2 maintainers
metapathways_python v2.1
A pipeline for MetaGenomic analysis which is capable of creating ePGDBs using Pathway Tools2 versions - Latest release: almost 10 years ago - 11 downloads last month - 2 maintainers
metagenome-atlas 2.0.0
ATLAS - workflows for assembly, annotation, and genomic binning of metagenomic and metatranscript...2 versions - Latest release: over 5 years ago - 1 dependent repositories - 31 downloads last month - 346 stars on GitHub - 2 maintainers
ancientmetagenomedircheck 1.2.1
Performs validity check of ancientMetagenomeDir datasets6 versions - Latest release: over 3 years ago - 40 downloads last month - 2 stars on GitHub - 1 maintainer
toolchest-client 0.11.14
Python client for Toolchest84 versions - Latest release: about 1 year ago - 1 dependent package - 2 dependent repositories - 456 downloads last month - 15 stars on GitHub - 3 maintainers
woltka 0.1.6
versatile meta-omic data classifier5 versions - Latest release: 3 months ago - 1 dependent repositories - 71 downloads last month - 64 stars on GitHub - 2 maintainers
Top 7.4% on pypi.org
48 versions - Latest release: 18 days ago - 2 dependent repositories - 403 downloads last month - 430 stars on GitHub - 3 maintainers
gtdbtk 2.4.0
A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.48 versions - Latest release: 18 days ago - 2 dependent repositories - 403 downloads last month - 430 stars on GitHub - 3 maintainers
magpurify 2.1.2
Identify and remove incorrectly binned contigs from metagenome-assembled genomes.5 versions - Latest release: about 4 years ago - 1 dependent repositories - 39 downloads last month - 44 stars on GitHub - 2 maintainers
kraken-biom 1.0.1
Create BIOM-format tables from Kraken output.1 version - Latest release: over 7 years ago - 1 dependent repositories - 96 downloads last month - 42 stars on GitHub - 2 maintainers
clark-biom 1.0.0
Create BIOM-format tables from CLARK abundance tables.1 version - Latest release: about 6 years ago - 1 dependent repositories - 34 downloads last month - 1 stars on GitHub - 1 maintainer
panphlan 1.3
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and *i...2 versions - Latest release: almost 4 years ago - 1 dependent repositories - 20 downloads last month - 39 stars on GitHub - 1 maintainer
metator 1.3.2
A pipeline for binning metagenomic datasets from metaHiC data.31 versions - Latest release: 6 months ago - 1 dependent repositories - 176 downloads last month - 20 stars on GitHub - 8 maintainers
pathogentrack 0.2.3
A pipeline to identify pathogenic microorganisms from scRNA-seq raw data1 version - Latest release: over 2 years ago - 1 dependent repositories - 23 downloads last month - 24 stars on GitHub - 2 maintainers
ymp 0.2.1
Flexible multi-omic pipeline system6 versions - Latest release: over 3 years ago - 1 dependent repositories - 60 downloads last month - 18 stars on GitHub - 2 maintainers
motulizer 0.3.2
making OTUs from genomes, and stats on them. and even core-genomes16 versions - Latest release: over 2 years ago - 1 dependent repositories - 123 downloads last month - 11 stars on GitHub - 1 maintainer
mgnify-pipelines-toolkit 0.1.2
Collection of scripts and tools for MGnify pipelines8 versions - Latest release: 15 days ago - 43 downloads last month - 1,561 stars on GitHub - 2 maintainers
taxamatcher 1.0.1
Easy to use taxonomy correlator1 version - Latest release: about 5 years ago - 1 dependent repositories - 8 downloads last month - 0 stars on GitHub - 2 maintainers
zol 1.2.1
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e....2 versions - Latest release: about 1 year ago - 27 downloads last month - 34 stars on GitHub - 1 maintainer
qadabra 0.3.0
Differential abundance workflow for microbiome data2 versions - Latest release: 4 months ago - 27 downloads last month - 14 stars on GitHub - 1 maintainer
metachip 1.10.13
HGT detection pipeline60 versions - Latest release: 12 months ago - 1 dependent repositories - 371 downloads last month - 49 stars on GitHub - 2 maintainers
micomplete 1.1.1
Quality control of assembled genomes9 versions - Latest release: almost 5 years ago - 1 dependent package - 1 dependent repositories - 52 downloads last month - 2 maintainers
genomeuploader 2.0.0
Python script to upload bins and MAGs in fasta format to ENA (European Nucleotide Archive). This ...1 version - Latest release: 16 days ago - 2 maintainers
fetch-tool 0.9.0
Utility to fetch public and private RAW read and assembly files from the ENA5 versions - Latest release: 8 months ago - 37 downloads last month - 2 stars on GitHub - 4 maintainers
macrel 1.3.0
MACREL6 versions - Latest release: 5 months ago - 1 dependent repositories - 20 downloads last month - 50 stars on GitHub - 2 maintainers
impy 0.2.8
Integrated Metaomic Pipeline command-line utility.13 versions - Latest release: about 7 years ago - 1 dependent repositories - 67 downloads last month - 1 maintainer
metasbt 0.1.2
A scalable framework for automatically indexing microbial genomes and accurately characterizing m...3 versions - Latest release: 12 months ago - 4 downloads last month - 0 stars on GitHub - 2 maintainers
metacoag 1.2.0
MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs6 versions - Latest release: 18 days ago - 23 downloads last month - 42 stars on GitHub - 1 maintainer
Top 8.7% on pypi.org
39 versions - Latest release: 3 months ago - 4 dependent repositories - 359 downloads last month - 172 stars on GitHub - 1 maintainer
insilicoseq 2.0.1
a sequencing simulator39 versions - Latest release: 3 months ago - 4 dependent repositories - 359 downloads last month - 172 stars on GitHub - 1 maintainer
gdmicro 1.0.10
GDmicro - Use GCN and Deep adaptation network to classify host disease status based on human gut ...10 versions - Latest release: 7 months ago - 70 downloads last month - 7 stars on GitHub - 2 maintainers
graphbin 1.7.1
graphbin: Refined binning of metagenomic contigs using assembly graphs.4 versions - Latest release: 10 months ago - 1 dependent repositories - 37 downloads last month - 81 stars on GitHub - 1 maintainer
superfocus 1.4.1
SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data8 versions - Latest release: over 2 years ago - 1 dependent repositories - 43 downloads last month - 19 stars on GitHub - 4 maintainers
muttui 2.0.2
A pipeline to reconstruct mutational spectra for bacterial and viral datasets3 versions - Latest release: almost 2 years ago - 24 downloads last month - 24 stars on GitHub - 2 maintainers
sixgill 0.2.4
six-frame genome-inferred libraries for LC-MS/MS8 versions - Latest release: over 7 years ago - 2 dependent repositories - 26 downloads last month - 2 maintainers
binning-refiner 1.4.3
Binning_refiner4 versions - Latest release: over 3 years ago - 1 dependent repositories - 43 downloads last month - 30 stars on GitHub - 2 maintainers
sgtree 0.0.10
Computational pipeline for fast and easy construction of phylogenetic trees.1 version - Latest release: over 3 years ago - 1 dependent repositories - 5 downloads last month - 2 maintainers
pyyamb 0.1.4
Yet Another Metagenome Binner8 versions - Latest release: 8 months ago - 61 downloads last month - 0 stars on GitHub - 1 maintainer
pnnl-atlas 1.0.32
ATLAS - a framework for assembly, annotation, and genomic binning of metagenomic and metatranscri...12 versions - Latest release: about 6 years ago - 1 dependent repositories - 70 downloads last month - 320 stars on GitHub - 2 maintainers
anvio 2.4.0
An interactive analysis and visualization platform for 'omics data. See https://merenlab.org/proj...29 versions - Latest release: almost 7 years ago - 2 dependent repositories - 85 downloads last month - 1 maintainer
amdirt 1.6.0
AMDirT: AncientMetagenomeDir Toolkit9 versions - Latest release: about 1 month ago - 1 dependent repositories - 316 downloads last month - 2 stars on GitHub - 2 maintainers
hgtsim 1.1.0
a simulator for HGT in microbial communities1 version - Latest release: over 5 years ago - 1 dependent repositories - 7 downloads last month - 8 stars on GitHub - 2 maintainers
metapathways 3.1.6
MetaPathways is a modular pipeline to build PGDBs from Metagenomic sequences.1 version - Latest release: over 3 years ago - 1 dependent repositories - 5 downloads last month - 0 stars on GitHub - 2 maintainers
gmgc-mapper 0.2.0
Map genes and genome to the Global Microbial Gene Catalog (GMGC)2 versions - Latest release: almost 4 years ago - 1 dependent repositories - 11 downloads last month - 6 stars on GitHub - 1 maintainer
hundo 1.2.8
Amplicon processing protocol31 versions - Latest release: almost 5 years ago - 1 dependent repositories - 187 downloads last month - 14 stars on GitHub - 2 maintainers
metaron 3.0
Metagenomic opeRon prediction pipeline4 versions - Latest release: about 2 years ago - 1 dependent repositories - 15 downloads last month - 6 stars on GitHub - 2 maintainers
spacegraphcats 2.1.2
tools for biological assembly graph neighborhood analysis15 versions - Latest release: over 1 year ago - 1 dependent repositories - 7 downloads last month - 114 stars on GitHub - 1 maintainer
magpurify2 1.0.2
Identify and remove contaminants from metagenome-assembled genomes.3 versions - Latest release: 12 months ago - 41 downloads last month - 14 stars on GitHub - 2 maintainers
cocopye 0.4.0
Feature-based prediction of genome quality indices11 versions - Latest release: 3 months ago - 66 downloads last month - 1 stars on GitHub - 2 maintainers
phageboost 0.1.7
a Fast Prophage and Phage Predictor5 versions - Latest release: over 3 years ago - 1 dependent repositories - 50 downloads last month - 32 stars on GitHub - 2 maintainers
combined-gene-caller 1.0.4
Combined gene caller for MGnify pipeline, to combine predictions from FragGeneScan and Prodigal2 versions - Latest release: 9 months ago - 6 downloads last month - 0 stars on GitHub - 4 maintainers
Related Keywords
bioinformatics
65
genomics
18
python
11
microbiome
9
binning
7
microbiology
7
Metagenomics
6
deep-learning
6
taxonomy
6
ngs
6
taxonomic-classification
6
assembly
5
snakemake
5
pipeline
5
machine-learning
4
Bioinformatics
4
bacteria
4
workflow
4
biology
4
pangenome
4
classification
4
k-mers
3
tool
3
alignment
3
ancient-dna
3
profiling
3
contigs
3
assembly-graphs
3
metagenome-assembly
3
metagenome-assembled genomes
3
comparative-genomics
3
annotation
3
metagenomic-pipeline
3
conda
3
clustering
3
metagenomic-classification
3
computational-biology
3
taxonomic-classifications
3
functional-annotation
3
NGS
3
viruses
2
hacktoberfest
2
Binning
2
Refinement
2
viral-metagenomics
2
rna-seq
2
microbial-genomics
2
phylogenetics
2
taxonomic
2
hgt
2
BIOM
2
clark
2
assembly-binning
2
self-supervised-learning
2
biom-format
2
kraken
2
sequencing
2
phage
2
genomic-binning
2
biosynthetic-gene-clusters
2
genome
2
ancient-metagenomics
2
data
2
palaeogenomics
2
lgt
2
16s
2
simulation
2
mmseqs
2
metatranscriptomics
2
virus
2
lateral-gene-transfer
2
ngless
2
metagenome-assembled-genomes
2
strains
2
deep
2
visualization
2
horizontal-gene-transfer
2
pgdb
1
rnaseq
1
bioconda
1
conda-environment
1
extensible
1
hacktoberfest-accepted
1
risk-assessment
1
hacktoberfest2022
1
multi-omics
1
omics-pipeline
1
ymp
1
antibiotic-resistance
1
mobile AMR
1
clinical AMR
1
cloud
1
hpc
1
r
1
single-cell-rna-seq
1
star
1
epgdb
1
archaea
1
nomenclature
1
pathwaytools
1