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aliview
|
public |
AliView is an intuitive and fast alignment viewer and editor for DNA and amino acid sequences.
|
2025-03-10 |
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cleanifier
|
public |
A fast lightweight tool to remove contamination using k-mers.
|
2025-03-10 |
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severus
|
public |
A tool for somatic structural variant calling using long reads
|
2025-03-10 |
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hmftools-esvee
|
public |
Structural variant caller specialised for breakend-breakpoint calling.
|
2025-03-10 |
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hmftools-linx
|
public |
LINX is an annotation, interpretation and visualisation tool for structural variants.
|
2025-03-10 |
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hmftools-pave
|
public |
PAVE annotates SNV/MNV/INDEL calls with consequence on corresponding genes, transcripts, and proteins.
|
2025-03-10 |
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r-pathosurveilr
|
public |
Utilities for interacting with the pathogensurveillance pipeline.
|
2025-03-10 |
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grepq
|
public |
Quickly filter FASTQ files.
|
2025-03-09 |
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olivar
|
public |
Olivar PCR tiling design
|
2025-03-09 |
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captus
|
public |
Captus: Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
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2025-03-09 |
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artic
|
public |
ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore.
|
2025-03-09 |
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pybwa
|
public |
Pybwa is a python module that makes it easy to align sequence data. It is a lightweight wrapper of bwa.
|
2025-03-08 |
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galaxy-data
|
public |
The Galaxy models, datatype framework, and datatype implementations.
|
2025-03-08 |
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galaxy-files
|
public |
The Galaxy file sources framework and default plugins.
|
2025-03-08 |
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galaxy-objectstore
|
public |
The Galaxy object store framework and default implementations
|
2025-03-08 |
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galaxy-schema
|
public |
The Galaxy API schema objects.
|
2025-03-08 |
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postmaster
|
public |
Postmaster is a tool for annotating transcriptome alignments with posterior alignment probabilities derived from salmon quantifications.
|
2025-03-08 |
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danbing-tk
|
public |
Toolkit for VNTR genotyping and repeat-pan genome graph construction
|
2025-03-08 |
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longbow
|
public |
A Python program for nanopore sequencing basecalling configuration prediction
|
2025-03-08 |
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miniprot
|
public |
Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.
|
2025-03-08 |
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last
|
public |
LAST finds & aligns related regions of sequences.
|
2025-03-07 |
|
gmap
|
public |
Genomic mapping and alignment program for mRNA and EST sequences.
|
2025-03-07 |
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callingcardstools
|
public |
An API and collection of cmd line tools to work with calling cards sequencing data
|
2025-03-07 |
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taxtastic
|
public |
Tools for taxonomic naming and annotation
|
2025-03-07 |
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r-signac
|
public |
A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart and Butler et al. (2019) <doi:10.1016/j.cell.2019.05.031>.
|
2025-03-07 |
|
cctk
|
public |
Tools to identify and compare CRISPR arrays.
|
2025-03-07 |
|
r-psminer
|
public |
Utilities for interacting with the pathogensurveillance pipeline.
|
2025-03-07 |
|
busco
|
public |
Assessment of assembly completeness using Universal Single Copy Orthologs.
|
2025-03-07 |
|
omark
|
public |
OMArk - Proteome quality assesment based on OMAmer placements
|
2025-03-07 |
|
perl-bio-phylo-forest-dbtree
|
public |
DBIx::Class-backed, Bio::Phylo-like API for large phylogenies.
|
2025-03-07 |
|
wfmash
|
public |
a pangenome-scale aligner
|
2025-03-07 |
|
te-aid
|
public |
Annotation helper tool for the manual curation of transposable element consensus sequences
|
2025-03-07 |
|
bioblend
|
public |
A Python library for interacting with the Galaxy API.
|
2025-03-07 |
|
hmftools-cuppa
|
public |
Predict tissue of origin for tumor samples from WGTS data.
|
2025-03-07 |
|
pegas
|
public |
PeGAS is a Snakemake pipeline for genome analysis
|
2025-03-07 |
|
snakemake-executor-plugin-kubernetes
|
public |
A snakemake executor plugin for submission of jobs to Kubernetes
|
2025-03-07 |
|
ebolaseq
|
public |
Tool for downloading and analyzing Ebola virus sequences
|
2025-03-07 |
|
bioconductor-dada2
|
public |
Accurate, high-resolution sample inference from amplicon sequencing data
|
2025-03-07 |
|
centrifuger
|
public |
Lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.
|
2025-03-07 |
|
resistify
|
public |
A resistance gene annotation tool.
|
2025-03-07 |
|
plannotate
|
public |
Webserver and command line tool for annotating engineered plasmids
|
2025-03-07 |
|
viroconstrictor
|
public |
ViroConstrictor is a flexible pipeline for analysis of targeted viral sequencing data
|
2025-03-07 |
|
snp2cell
|
public |
A package for finding enriched regulatory networks from GWAS and single cell data.
|
2025-03-07 |
|
savana
|
public |
SAVANA: a somatic structural variant caller for long-read data
|
2025-03-07 |
|
bioconductor-glmgampoi
|
public |
Fit a Gamma-Poisson Generalized Linear Model
|
2025-03-06 |
|
gmap-fusion
|
public |
GMAP-fusion is a utility for identifying candidate fusion transcripts based on transcript sequences reconstructed via RNA-Seq de novo transcriptome assembly.
|
2025-03-06 |
|
transdecoder
|
public |
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
|
2025-03-06 |
|
fusion-filter
|
public |
FusionFilter provides a common fusion-finding, filtering, and annotation framework for the Trinity Cancer Transcriptome Analysis Toolkit (CTAT).
|
2025-03-06 |
|
fusion-inspector
|
public |
FusionInspector is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). FusionInspector assists in fusion transcript discovery by performing a supervised analysis of fusion predictions, attempting to recover and re-score evidence for such predictions. - https://github.com/FusionInspector/FusionInspector/wiki
|
2025-03-06 |
|
flexynesis
|
public |
A deep-learning-based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.
|
2025-03-06 |
