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plass
|
public |
Plass (Protein-Level ASSembler) and PenguiN (Protein-guided Nucleotide assembler) are methods to assemble short read sequencing data on a protein level to proteins or DNA contigs
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2024-07-11 |
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bedtools
|
public |
A powerful toolset for genome arithmetic
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2024-07-10 |
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fasttree
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public |
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences
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2024-07-10 |
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pysam
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public |
Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.
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2024-07-10 |
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bamtools
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public |
C++ API & command-line toolkit for working with BAM data
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2024-07-10 |
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bioawk
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public |
BWK awk modified for biological data
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2024-07-10 |
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locarna
|
public |
Multiple alignment of RNAs
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2024-07-10 |
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selene-sdk
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public |
Framework for developing sequence-level deep learning networks.
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2024-07-10 |
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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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2024-07-09 |
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fasta3
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public |
The FASTA package - protein and DNA sequence similarity searching and alignment programs
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2024-07-09 |
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cpat
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public |
Coding Potential Assessment Tool
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2024-07-09 |
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somaticseq
|
public |
An ensemble approach to accurately detect somatic mutations
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2024-07-09 |
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sentieon
|
public |
Accelerated performance bioinformatics tools for mapping and variant calling
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2024-07-09 |
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arvados-python-client
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public |
Python API for Arvados
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2024-07-09 |
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sniffles
|
public |
Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore)
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2024-07-08 |
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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
|
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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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
|
2024-07-04 |
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survivor
|
public |
Toolset for SV simulation, comparison and filtering
|
2024-07-03 |
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star
|
public |
An RNA-seq read aligner.
|
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
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2024-07-02 |
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r-biodb
|
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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extract_fullseq
|
public |
extract_fullseq is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets
|
2024-07-01 |
|
squizz
|
public |
Squizz is a sequence/alignment format checker, but it has some conversion capabilities too.
|
2024-07-01 |
|
expansionhunter
|
public |
A tool for estimating repeat sizes
|
2024-07-01 |
|
hicexplorer
|
public |
Set of programs to process, analyze and visualize Hi-C and capture Hi-C data
|
2024-06-28 |
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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 |
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bmfilter
|
public |
bmfilter is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets
|
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 |
|
plink2
|
public |
Whole genome association analysis toolset
|
2024-06-28 |
|
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 |
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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 |
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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 |
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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 |
|
lrzip
|
public |
Long Range ZIP or Lzma RZIP. This is a compression program optimised for large files. The larger the file and the more memory you have, the better the compression advantage this will provide, especially once the files are larger than 100MB. The advantage can be chosen to be either size (much smaller than bzip2) or speed (much faster than bzip2).
|
2024-06-24 |
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pyprophet
|
public |
Python reimplementation of mProphet peak scoring
|
2024-06-24 |
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ngmlr
|
public |
ngmlr is a long-read mapper designed to align PacBio or Oxford Nanopore reads to a reference genome and optimized for structural variation detection
|
2024-06-23 |
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dsrc
|
public |
high-performance compression of sequencing reads stored in FASTQ format
|
2024-06-21 |
