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neptune-signature
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public |
Neptune: Genomic Signature Discovery
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2024-11-20 |
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crabs
|
public |
Crabs (Creating Reference databases for Amplicon-Based Sequencing) is a program to download and curate reference databases for eDNA metabarcoding analyses.
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2024-11-20 |
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svtopo
|
public |
Complex structural variant visualization for HiFi sequencing data: extraction tool
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2024-11-20 |
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search_ncbi
|
public |
A package for searching and processing NCBI data
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2024-11-19 |
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mvip
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public |
MVP v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes and isolate genomes.
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2024-11-19 |
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hicstuff
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public |
General purpose stuff to generate and handle Hi-C data in its simplest form.
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2024-11-19 |
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hisat2-pipeline
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public |
A pipeline to automatically run an RNA-seq analysis using HISAT2/Stringtie using default settings.
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2024-11-19 |
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snpick
|
public |
A fast and memory-efficient tool for SNP extraction from genomic alignments.
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2024-11-19 |
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cazy_webscraper
|
public |
A tool to automate retrieving data from CAZy, build a local CAZyme SQL database, and throughly interrogating the data. Also, automate retrieving protein data, sequences, EC numbers and structure files for specific datasets in the CAZyme database from UniProt, GenBank and PDB.
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2024-11-19 |
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svtopovz
|
public |
Complex structural variant visualization for HiFi sequencing data: plotting tool.
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2024-11-19 |
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commec
|
public |
commec: a free, open-source, globally available tool for DNA sequence screening
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2024-11-19 |
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parm
|
public |
promoter activity regulatory model
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2024-11-19 |
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treeswift
|
public |
TreeSwift: Fast tree module for Python 2 and 3
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2024-11-19 |
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minute
|
public |
MINUTE-ChIP data analysis workflow
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2024-11-19 |
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panfeed
|
public |
Compute gene-cluster specific k-mers over a pangenome
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2024-11-19 |
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ampcombi
|
public |
A parsing tool to convert and summarise the outputs from multiple AMP detection tools.
|
2024-11-19 |
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lsabgc
|
public |
lsaBGC-Pan - refined workflow for pan-BGC-omic evolutionary investigations.
|
2024-11-19 |
|
instanovo
|
public |
De novo peptide sequencing with InstaNovo
|
2024-11-19 |
|
unikseq
|
public |
Unique DNA sequence region identification using a k-mer approach
|
2024-11-18 |
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cnvkit
|
public |
Copy number variant detection from high-throughput sequencing.
|
2024-11-18 |
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kestrel
|
public |
Mapping-free variant caller for short-read Illumina data
|
2024-11-16 |
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jaeger-bio
|
public |
A quick and precise pipeline for detecting phages in sequence assemblies.
|
2024-11-15 |
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zamp
|
public |
zAMP: bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
|
2024-11-15 |
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merqury
|
public |
Evaluate genome assemblies with k-mers and more.
|
2024-11-15 |
|
krakentools
|
public |
KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
|
2024-11-15 |
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breakfast
|
public |
breakfast: fast putative outbreak cluster and infection chain detection using SNPs.
|
2024-11-15 |
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virheat
|
public |
Visualize microbial evolution at the SNP level by creating a heatmap from vcf files.
|
2024-11-15 |
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biobb_chemistry
|
public |
Biobb_chemistry is the Biobb module collection to perform chemical conversions.
|
2024-11-15 |
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biobb_dna
|
public |
Biobb_dna is a package composed of different analyses for nucleic acid trajectories.
|
2024-11-15 |
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beagle
|
public |
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
|
2024-11-14 |
|
get_homologues
|
public |
A versatile software package for pan-genome analysis, including GET_HOMOLOGUES and GET_HOMOLOGUES-EST
|
2024-11-14 |
|
snipit
|
public |
Visualize snps relative to a reference sequence
|
2024-11-13 |
|
teloclip
|
public |
A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
|
2024-11-13 |
|
biobb_analysis
|
public |
Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.
|
2024-11-12 |
|
coptr
|
public |
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
|
2024-11-12 |
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orthodb
|
public |
Interface to OrthoDB REST API.
|
2024-11-12 |
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dnaio
|
public |
Read and write FASTA and FASTQ files efficiently
|
2024-11-12 |
|
cellprofiler
|
public |
CellProfiler is free, open-source software for quantitative analysis of biological images.
|
2024-11-12 |
|
matchms
|
public |
Python library for fuzzy comparison of mass spectrum data and other Python objects
|
2024-11-12 |
|
metaphor
|
public |
Metaphor - Metagenomic Pipeline for Short Reads
|
2024-11-11 |
|
lamps
|
public |
Liverpool Annotation of metabolites using Mass Spectrometry
|
2024-11-10 |
|
r-remapenrich
|
public |
Bioinformatics tools to compute statistical enrichment of geonomic regions for ReMap peaks
|
2024-11-10 |
|
gadma
|
public |
Genetic Algorithm for Demographic Inference
|
2024-11-07 |
|
bioblend
|
public |
A Python library for interacting with the Galaxy API.
|
2024-11-07 |
|
bam2plot
|
public |
Plot of coverage from bam file
|
2024-11-07 |
|
sigprofilermatrixgenerator
|
public |
SigProfiler matrix generator tool.
|
2024-11-07 |
|
trtools
|
public |
Toolkit for genome-wide analysis of tandem repeats
|
2024-11-07 |
|
zdb
|
public |
zDB is both a bacterial comparative genomics pipeline and a tool to visualize the results
|
2024-11-06 |
|
bftools
|
public |
Bio-Formats Command line tools
|
2024-11-06 |
|
argparse2tool
|
public |
Instrument for forming Galaxy XML and CWL tool descriptions from argparse arguments
|
2024-11-05 |
