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treetime
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public |
Maximum-Likelihood dating and ancestral inference for phylogenetic trees
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2024-07-07 |
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snakemake
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
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2024-07-06 |
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snakemake-minimal
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
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2024-07-06 |
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manta
|
public |
Structural variant and indel caller for mapped sequencing data
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2024-07-05 |
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ribotaper
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public |
RiboTaper is a new analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.
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2024-07-05 |
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iqtree
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public |
Efficient phylogenomic software by maximum likelihood.
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2024-07-04 |
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sambamba
|
public |
Tools for working with SAM/BAM data
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2024-07-04 |
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metasnv
|
public |
SNV calling software
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2024-07-04 |
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ucsc-cell-browser
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public |
A browser for single-cell data, main site at http://cells.ucsc.edu. UCSC Cellbrowser, an interactive browser for single cell data. Includes importers and basic pipelines for text files, Seurat, Scanpy and Cellranger. All Javascript - does not require a server backend.
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2024-07-04 |
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survivor
|
public |
Toolset for SV simulation, comparison and filtering
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2024-07-03 |
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star
|
public |
An RNA-seq read aligner.
|
2024-07-03 |
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taxonkit
|
public |
A Cross-platform and Efficient NCBI Taxonomy Toolkit
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2024-07-03 |
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trimal
|
public |
A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment
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2024-07-03 |
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bwakit
|
public |
A self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping
|
2024-07-02 |
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r-biodb
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public |
An R package for connecting to chemical and biological databases.
|
2024-07-02 |
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slclust
|
public |
A utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters.
|
2024-07-02 |
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chewbbaca
|
public |
A complete suite for gene-by-gene schema creation and strain identification.
|
2024-07-02 |
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extract_fullseq
|
public |
extract_fullseq is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets
|
2024-07-01 |
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squizz
|
public |
Squizz is a sequence/alignment format checker, but it has some conversion capabilities too.
|
2024-07-01 |
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expansionhunter
|
public |
A tool for estimating repeat sizes
|
2024-07-01 |
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sourmash
|
public |
Compute and compare MinHash signatures for DNA data sets.
|
2024-06-30 |
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nonpareil
|
public |
Estimate average coverage and create curves for metagenomic datasets
|
2024-06-28 |
|
hicexplorer
|
public |
Set of programs to process, analyze and visualize Hi-C and capture Hi-C data
|
2024-06-28 |
|
merfishtools
|
public |
MERFISHtools implement a Bayesian framework for accurately predicting gene or transcript expression from MERFISH data. On top, differential expression analysis can be performed for two or multiple conditions, including credible intervals for fold change and coefficient of variation, and controlling the expected false discovery rate.
|
2024-06-28 |
|
sonicparanoid
|
public |
SonicParanoid: fast, accurate, and comprehensive orthology inference with machine learning and language models
|
2024-06-28 |
|
bmfilter
|
public |
bmfilter is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets
|
2024-06-28 |
|
cgpbigwig
|
public |
BigWig manpulation tools using libBigWig and htslib
|
2024-06-28 |
|
snp-dists
|
public |
Convert a FASTA alignment to SNP distance matrix
|
2024-06-28 |
|
bmtool
|
public |
bmtool is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets
|
2024-06-28 |
|
pairtools
|
public |
CLI tools to process mapped Hi-C data
|
2024-06-28 |
|
ngs-disambiguate
|
public |
Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem
|
2024-06-28 |
|
srprism
|
public |
SRPRISM - Short Read Alignment Tool
|
2024-06-28 |
|
gappa
|
public |
Genesis Applications for Phylogenetic Placement Analysis
|
2024-06-28 |
|
perl-graph
|
public |
a Perl extension for keeping data partially sorted
|
2024-06-28 |
|
plink2
|
public |
Whole genome association analysis toolset
|
2024-06-28 |
|
ngs-bits
|
public |
Short-read sequencing tools
|
2024-06-27 |
|
picard
|
public |
Java tools for working with NGS data in the BAM format
|
2024-06-27 |
|
wiggletools
|
public |
The WiggleTools package allows genomewide data files to be manipulated as numerical functions, equipped with all the standard functional analysis operators (sum, product, product by a scalar, comparators), and derived statistics (mean, median, variance, stddev, t-test, Wilcoxon's rank sum test, etc).
|
2024-06-27 |
|
delly
|
public |
Structural variant discovery by integrated paired-end and split-read analysis
|
2024-06-27 |
|
gdc-client
|
public |
GDC Data Transfer Tool
|
2024-06-27 |
|
idba
|
public |
IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.
|
2024-06-26 |
|
cansam
|
public |
C++ binding for SAM/BAM files
|
2024-06-26 |
|
checkm-genome
|
public |
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
|
2024-06-26 |
|
rnaquast
|
public |
rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.
|
2024-06-25 |
|
idr
|
public |
The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.
|
2024-06-25 |
|
snap-aligner
|
public |
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
|
2024-06-25 |
|
tandem-genotypes
|
public |
Find tandem repeat length changes, from "long" DNA reads aligned to a genome
|
2024-06-25 |
|
kaptive
|
public |
Reports information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies.
|
2024-06-25 |
|
mason
|
public |
Mason is a collection of tools for the simulation of biological sequences.
|
2024-06-24 |
|
abyss
|
public |
Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler
|
2024-06-24 |
