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snakemake-wrapper-utils
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public |
A collection of utility functions and classes for Snakemake wrappers.
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2025-03-21 |
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quantms-rescoring
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public |
PSM rescoring python package with scripts and helpers for the quantms workflow
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2025-03-21 |
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clair3
|
public |
Clair3 is a small variant caller for long-reads. Compare to PEPPER (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data (precisionFDA Truth Challenge V2), and a better Indel F1-score, while runs generally four times faster. Clair3 makes the best of both worlds of using pileup or full-alignment as input for deep-learning based long-read small variant calling. Clair3 is simple and modular for easy deployment and integration.
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2025-03-21 |
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pypolca
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public |
Standalone Python re-implementation of the POLCA polisher from MaSuRCA
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2025-03-21 |
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rtg-tools
|
public |
RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation
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2025-03-21 |
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spacedust
|
public |
De novo discovery of conserved gene clusters in microbial genomes with Spacedust
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2025-03-21 |
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bioconda-repodata-patches
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public |
generate tweaks to index metadata, hosted separately from anaconda.org index
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2025-03-21 |
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fastga
|
public |
FastGA - A Fast Genome Aligner.
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2025-03-20 |
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snakemake-minimal
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
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2025-03-20 |
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snakemake
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
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2025-03-20 |
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snakemake-storage-plugin-fs
|
public |
A Snakemake storage plugin that reads and writes from a locally mounted filesystem using rsync.
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2025-03-20 |
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mi-pimento
|
public |
A PrIMEr infereNce TOolkit to facilitate large-scale calling of metabarcoding amplicon sequence variants
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2025-03-20 |
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cctyper
|
public |
CRISPRCasTyper: Automatic detection and subtyping of CRISPR-Cas operons
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2025-03-20 |
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dbcan
|
public |
Standalone version of dbCAN annotation tool for automated CAZyme annotation.
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2025-03-20 |
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ntm-profiler
|
public |
Profiling tool for NTM to detect species and resistance from WGS data
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2025-03-20 |
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semibin
|
public |
Metagenomic binning with siamese neural networks
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2025-03-20 |
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firecloud
|
public |
API and CLI for Broad Institute's Firecloud workspace/workflow management service.
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2025-03-20 |
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binette
|
public |
A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.
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2025-03-20 |
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fgpyo
|
public |
Python bioinformatics and genomics library
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2025-03-20 |
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bioconductor-scdblfinder
|
public |
scDblFinder
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2025-03-20 |
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bioconductor-scater
|
public |
Single-Cell Analysis Toolkit for Gene Expression Data in R
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2025-03-20 |
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bioconductor-scds
|
public |
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
|
2025-03-20 |
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snakemake-interface-storage-plugins
|
public |
This package provides a stable interface for interactions between Snakemake and its storage plugins.
|
2025-03-20 |
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caspeak
|
public |
A pipeline for finding non-reference mobile element insertions
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2025-03-20 |
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nextclade
|
public |
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
|
2025-03-20 |
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metagenome-atlas
|
public |
ATLAS - Three commands to start analysing your metagenome data
|
2025-03-20 |
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snakemake-interface-logger-plugins
|
public |
This package provides a stable interface for interactions between Snakemake and its logger plugins.
|
2025-03-20 |
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nrpys
|
public |
Python language bindings for nrps-rs substrate specificity predictor.
|
2025-03-20 |
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shiba2sashimi
|
public |
A utility for creating sashimi plot from Shiba output
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2025-03-20 |
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plasann
|
public |
A tool for plasmid annotation and visualization
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2025-03-20 |
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hyphy
|
public |
An open-source software package for comparative sequence analysis using stochastic evolutionary models.
|
2025-03-20 |
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nanocaller
|
public |
NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing.
|
2025-03-20 |
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corgi
|
public |
Classifier for ORganelle Genomes Inter alia
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2025-03-20 |
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somaticseq
|
public |
An ensemble approach to accurately detect somatic mutations.
|
2025-03-19 |
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nda-tools
|
public |
Python package for interacting with NDA web services.
|
2025-03-19 |
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perl-extutils-depends
|
public |
Easily build XS extensions that depend on XS extensions.
|
2025-03-19 |
|
ezomero
|
public |
A module with convenience functions for writing Python code that interacts with OMERO.
|
2025-03-19 |
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latch
|
public |
The Latch python bioinformatics framework
|
2025-03-19 |
|
wakhan
|
public |
A tool to analyze haplotype-specific chromosome-scale somatic copy number aberrations and aneuploidy using long reads
|
2025-03-19 |
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pytrf
|
public |
a fast Python package for finding tandem repeat sequences
|
2025-03-19 |
|
fusion-report
|
public |
Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline
|
2025-03-19 |
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bioconductor-lpsymphony
|
public |
Symphony integer linear programming solver in R
|
2025-03-19 |
|
repeatmasker
|
public |
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
|
2025-03-19 |
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bioconductor-flowworkspace
|
public |
Infrastructure for representing and interacting with gated and ungated cytometry data sets.
|
2025-03-19 |
|
ngs-bits
|
public |
Short-read sequencing tools
|
2025-03-19 |
|
npstructures
|
public |
Simple data structures that augments the numpy library
|
2025-03-19 |
|
bioconductor-cellnoptr
|
public |
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
|
2025-03-19 |
|
bioconductor-rgadem
|
public |
de novo motif discovery
|
2025-03-19 |
|
bioconductor-rbowtie
|
public |
R bowtie wrapper
|
2025-03-19 |
|
bioconductor-deepsnv
|
public |
Detection of subclonal SNVs in deep sequencing data.
|
2025-03-19 |
