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gubbins
|
public |
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
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2025-03-18 |
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fgbio
|
public |
A set of tools for working with genomic and high throughput sequencing data, including UMIs
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2025-03-18 |
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dsh-bio
|
public |
Tools for BED, FASTA, FASTQ, GAF, GFA1/2, GFF3, PAF, SAM, and VCF files
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2025-03-18 |
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canu
|
public |
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing.
|
2025-03-17 |
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perl-xml-libxslt
|
public |
Interface to GNOME libxslt library
|
2025-03-17 |
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python-newick
|
public |
A python module to read and write the Newick format.
|
2025-03-17 |
|
illumina-interop
|
public |
The Illumina InterOp libraries are a set of common routines used for reading and writing InterOp metric files. These metric files are binary files produced during a run providing detailed statistics about a run. In a few cases, the metric files are produced after a run during secondary analysis (index metrics) or for faster display of a subset of the original data (collapsed quality scores).
|
2025-03-17 |
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pybedtools
|
public |
Wraps BEDTools for use in Python and adds many additional features.
|
2025-03-17 |
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ectyper
|
public |
ECtyper is a python program for serotyping E. coli genomes
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2025-03-15 |
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hyphy
|
public |
An open-source software package for comparative sequence analysis using stochastic evolutionary models.
|
2025-03-15 |
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kraken
|
public |
Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
|
2025-03-14 |
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perl-io-compress
|
public |
IO Interface to compressed data files/buffers
|
2025-03-14 |
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bioconductor-gsva
|
public |
Gene Set Variation Analysis for Microarray and RNA-Seq Data
|
2025-03-13 |
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perl-data-dump
|
public |
Pretty printing of data structures
|
2025-03-13 |
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percolator
|
public |
Semi-supervised learning for peptide identification from shotgun proteomics datasets.
|
2025-03-13 |
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xsd
|
public |
No Summary
|
2025-03-13 |
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r-ggbiplot
|
public |
A biplot based on ggplot2
|
2025-03-13 |
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python-edlib
|
public |
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
|
2025-03-13 |
|
r-lncpipereporter
|
public |
Automatically Aggregating and Summarizing lncRNA Analysis Results for Interactive Report
|
2025-03-13 |
|
miranda
|
public |
An algorithm for finding genomic targets for microRNAs
|
2025-03-12 |
|
plek
|
public |
Predictor of long non-coding RNAs and mRNAs based on k-mer scheme.
|
2025-03-12 |
|
seqkit
|
public |
a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
|
2025-03-12 |
|
taxonkit
|
public |
A Cross-platform and Efficient NCBI Taxonomy Toolkit
|
2025-03-12 |
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perl-list-moreutils-xs
|
public |
Provide the stuff missing in List::Util in XS
|
2025-03-12 |
|
sniffles
|
public |
Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore).
|
2025-03-12 |
|
eggnog-mapper
|
public |
Fast genome-wide functional annotation through orthology assignment.
|
2025-03-11 |
|
wgsim
|
public |
No Summary
|
2025-03-11 |
|
segemehl
|
public |
Short read mapping with gaps
|
2025-03-11 |
|
pear
|
public |
paired-end read merger
|
2025-03-11 |
|
snakemake
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
|
2025-03-11 |
|
snakemake-minimal
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
|
2025-03-11 |
|
pysamstats
|
public |
A Python utility for calculating statistics against genome position based on sequence alignments from a SAM, BAM or CRAM file.
|
2025-03-11 |
|
meme
|
public |
Motif-based sequence analysis tools.
|
2025-03-11 |
|
smallgenomeutilities
|
public |
A collection of scripts that are useful for dealing with viral RNA NGS data.
|
2025-03-10 |
|
presto
|
public |
A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
|
2025-03-10 |
|
dxpy
|
public |
DNAnexus Platform API bindings for Python
|
2025-03-10 |
|
perl-cgi
|
public |
A generic file fetching mechanism.
|
2025-03-10 |
|
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 |
|
taxtastic
|
public |
Tools for taxonomic naming and annotation
|
2025-03-07 |
|
busco
|
public |
Assessment of assembly completeness using Universal Single Copy Orthologs.
|
2025-03-07 |
|
bioblend
|
public |
A Python library for interacting with the Galaxy API.
|
2025-03-07 |
|
bioconductor-dada2
|
public |
Accurate, high-resolution sample inference from amplicon sequencing data
|
2025-03-07 |
|
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 |
|
ensembl-vep
|
public |
Ensembl Variant Effect Predictor
|
2025-03-05 |
|
bam-readcount
|
public |
bam-readcount generates metrics at single nucleotide positions.
|
2025-03-05 |
|
plink
|
public |
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
|
2025-03-04 |
