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treeswift
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public |
TreeSwift: Fast tree module for Python 2 and 3
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2024-11-19 |
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jbrowse2
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public |
The JBrowse 2 Genome Browser
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2024-11-19 |
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minute
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public |
MINUTE-ChIP data analysis workflow
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2024-11-19 |
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notramp
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public |
Super-fast Normalization and Trimming for Amplicon Sequencing Data (Long- and Short-read)
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2024-11-19 |
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libcifpp
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public |
Library containing code to manipulate mmCIF and PDB files.
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2024-11-19 |
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panfeed
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public |
Compute gene-cluster specific k-mers over a pangenome
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2024-11-19 |
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ampcombi
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public |
A parsing tool to convert and summarise the outputs from multiple AMP detection tools.
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2024-11-19 |
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lsabgc
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public |
lsaBGC-Pan - refined workflow for pan-BGC-omic evolutionary investigations.
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2024-11-19 |
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poppunk
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public |
PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
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2024-11-19 |
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biobb_godmd
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public |
Biobb_godmd is a BioBB category for GOdMD tool (protein conformational transitions).
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2024-11-19 |
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perl-io-compress
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public |
IO Interface to compressed data files/buffers
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2024-11-19 |
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instanovo
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public |
De novo peptide sequencing with InstaNovo
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2024-11-19 |
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unikseq
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public |
Unique DNA sequence region identification using a k-mer approach
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2024-11-18 |
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nextflow
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public |
A DSL for data-driven computational pipelines http://nextflow.io
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2024-11-18 |
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gfainject
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public |
Inject alignment into pangenome graphs
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2024-11-18 |
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pathogen-profiler
|
public |
Library giving access to classes and functions to create a profiling tool to look for mutations from NGS data.
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2024-11-18 |
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snk-cli
|
public |
Dynamically generate CLIs from Snakemake configuration files
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2024-11-18 |
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muse
|
public |
An accurate and ultra-fast somatic point mutation calling tool for whole-genome sequencing (WGS) and whole-exome sequencing (WES) data from heterogeneous tumor samples.
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2024-11-18 |
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isoquant
|
public |
IsoQuant is a tool for reference-based analysis of long RNA reads, such as gene/transcript quantification and discovery.
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2024-11-18 |
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cnvkit
|
public |
Copy number variant detection from high-throughput sequencing.
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2024-11-18 |
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biobambam
|
public |
Tools for early stage alignment file processing.
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2024-11-18 |
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libmaus2
|
public |
Collection of data structures and algorithms for NGS data.
|
2024-11-18 |
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rdeval
|
public |
A general purpose, multithreaded read analysis and manipulation tool.
|
2024-11-17 |
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zol
|
public |
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters.
|
2024-11-16 |
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r-locuszoomr
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public |
Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots.
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2024-11-16 |
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kestrel
|
public |
Mapping-free variant caller for short-read Illumina data
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2024-11-16 |
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bakta
|
public |
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
|
2024-11-16 |
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tttrlib
|
public |
A file format agnostic library for time-resolved imaging and spectroscopic data.
|
2024-11-15 |
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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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r-facets
|
public |
Cellular Fraction and Copy Numbers from Tumor Sequencing
|
2024-11-15 |
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sfold
|
public |
Software for Statistical Folding of Nucleic Acids
|
2024-11-15 |
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perl-class-methodmaker
|
public |
Create generic methods for OO Perl
|
2024-11-15 |
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hmftools-redux
|
public |
Post-processing read alignments to control sequencing errors and biases
|
2024-11-15 |
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merqury
|
public |
Evaluate genome assemblies with k-mers and more.
|
2024-11-15 |
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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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gubbins
|
public |
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
|
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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argo
|
public |
Argo: species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping
|
2024-11-15 |
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ebi-eva-common-pyutils
|
public |
EBI EVA - Common Python Utilities
|
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 |
|
beagle
|
public |
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
|
2024-11-14 |
|
itsxpress
|
public |
ITSxpress: Software to rapidly trim the Internally Transcribed Spacer (ITS) region from FASTQ files
|
2024-11-14 |
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fibertools-rs
|
public |
Mitchell Vollger's rust tools for fiberseq data.
|
2024-11-14 |
|
fairy
|
public |
fairy calculates all-to-all approximate coverage for multi-sample metagenomic binning > 100x faster than alignment.
|
2024-11-14 |
|
get_homologues
|
public |
A versatile software package for pan-genome analysis, including GET_HOMOLOGUES and GET_HOMOLOGUES-EST
|
2024-11-14 |
|
hybracter
|
public |
An automated long-read first bacterial genome assembly pipeline.
|
2024-11-14 |
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gseapy
|
public |
Gene Set Enrichment Analysis in Python
|
2024-11-13 |
