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thapbi-pict
|
public |
THAPBI Phytophthora ITS1 Classifier Tool (PICT).
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2024-09-09 |
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snakemake-executor-plugin-drmaa
|
public |
A snakemake executor plugin for submission of jobs via DRMAA.
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2024-09-09 |
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snakemake-executor-plugin-kubernetes
|
public |
A snakemake executor plugin for submission of jobs to Kubernetes
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2024-09-09 |
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binchicken
|
public |
Targeted recovery of low abundance metagenome assembled genomes through intelligent coassembly
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2024-09-09 |
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biobox_add_taxid
|
public |
CAMI amber utility script for adding the taxid output from GTDB and BAT
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2024-09-08 |
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clinvar-this
|
public |
ClinVar Submission API Made Easy
|
2024-09-07 |
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cogent3
|
public |
COmparative GENomics Toolkit 3: genomic sequence analysis within notebooks or on compute systems with 1000s of CPUs.
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2024-09-06 |
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scnic
|
public |
SCNIC: Sparse Cooccurence Network Investigation for Compositional data
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2024-09-06 |
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piawka
|
public |
The powerful AWK script to calculate population statistics in VCF files with support for varying ploidy and missing data
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2024-09-06 |
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ipyrad
|
public |
Interactive assembly and analysis of RAD-seq data sets.
|
2024-09-06 |
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egglib
|
public |
Evolutionary Genetics and Genomics Library. EggLib is a C++/Python library and program package for evolutionary genetics and genomics. Main features are sequence data management, sequence polymorphism analysis, and coalescent simulations. EggLib is a flexible Python module with a performant underlying C++ library and allows fast and intuitive development of Python programs and scripts.
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2024-09-06 |
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treesimulator
|
public |
Simulation of rooted phylogenetic trees under a given Multitype Birth–Death (MTBD) model.
|
2024-09-06 |
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annonars
|
public |
Genome annotation based on Rust and RocksDB.
|
2024-09-06 |
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oakvar
|
public |
OakVar - Genomic Variant Analysis Platform
|
2024-09-06 |
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cami-amber
|
public |
AMBER: Assessment of Metagenome BinnERs
|
2024-09-06 |
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varvamp
|
public |
Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses
|
2024-09-06 |
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shorttracks
|
public |
ShortTracks : Useful length- and strand-based coverage files (bigwig) from small RNA-seq alignments (BAM)
|
2024-09-05 |
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r-anndata
|
public |
A 'reticulate' wrapper for the Python package 'anndata'. Provides a scalable way of keeping track of data and learned annotations. Used to read from and write to the h5ad file format.
|
2024-09-05 |
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strucvis
|
public |
strucVis : Display small RNA depth of coverage on a predicted RNA secondary structure
|
2024-09-05 |
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starcatpy
|
public |
Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs.
|
2024-09-05 |
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handyreadgenotyper
|
public |
Tool for training model and classifying reads from environmental ONT amplicon sequencing.
|
2024-09-05 |
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annotsv
|
public |
Annotation and Ranking of Structural Variation
|
2024-09-05 |
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cagee
|
public |
Analyzes changes in gene expression in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences
|
2024-09-05 |
|
binette
|
public |
A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.
|
2024-09-05 |
|
anchorwave
|
public |
Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication variation
|
2024-09-05 |
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python-edlib
|
public |
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
|
2024-09-05 |
|
piranha-polio
|
public |
Poliovirus Investigation Resource Automating Nanopore Haplotype Analysis
|
2024-09-05 |
|
allo
|
public |
Multi-mapped read rescue strategy for gene regulatory analyses
|
2024-09-05 |
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clipandmerge
|
public |
Clip&Merge is a tool to clip off adapters from sequencing reads and merge overlapping paired end reads together.
|
2024-09-05 |
|
dedup
|
public |
DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).
|
2024-09-05 |
|
bcbio-gff
|
public |
A Python library to read and write Generic Feature Format (GFF).
|
2024-09-05 |
|
flexi-formatter
|
public |
Moving flexiplex barcode and UMI to bam tags
|
2024-09-05 |
|
medicc2
|
public |
Whole-genome doubling-aware copy number phylogenies for cancer evolution
|
2024-09-04 |
|
poplddecay
|
public |
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format (VCF) files.
|
2024-09-04 |
|
pyrodigal
|
public |
Python bindings to Prodigal, an ORF finder for microbial sequences.
|
2024-09-04 |
|
beacon2-import
|
public |
Seamlessly import and query genomic variant data from a beacon
|
2024-09-04 |
|
pydeseq2
|
public |
A python implementation of DESeq2.
|
2024-09-04 |
|
pytrimal
|
public |
Cython bindings and Python interface to trimAl, a tool for automated alignment trimming.
|
2024-09-04 |
|
last
|
public |
LAST finds & aligns related regions of sequences.
|
2024-09-03 |
|
spaln
|
public |
Map and align a set of cDNA/EST or protein sequences onto a genome
|
2024-09-03 |
|
nextstrain-cli
|
public |
The Nextstrain command-line interface (CLI)
|
2024-09-03 |
|
jvarkit
|
public |
Java utilities for Bioinformatics.
|
2024-09-03 |
|
mehari
|
public |
VEP-like tool for sequence ontology and HGVS annotation of VCF files written in Rust.
|
2024-09-03 |
|
distle
|
public |
Fast distance matrix calculations on fasta and cgmlst files
|
2024-09-03 |
|
galah
|
public |
Galah aims to be a more scalable metagenome assembled genome (MAG) dereplication method.
|
2024-09-03 |
|
argo
|
public |
Argo: species-resolved profiling of antibiotic resistant genes with long-read metagenomics
|
2024-09-03 |
|
perl-graph
|
public |
a Perl extension for keeping data partially sorted
|
2024-09-02 |
|
mgnify-pipelines-toolkit
|
public |
Collection of scripts and tools for MGnify pipelines
|
2024-09-02 |
|
beav
|
public |
beav: Bacterial genome and mobile element annotation pipeline
|
2024-09-02 |
|
aviary
|
public |
End-to-end metagenomics hybrid assembly and binning pipeline.
|
2024-09-02 |
