1634 days ago
HaploTypo: a variant-calling pipeline for phased genomes
An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly account for haplotype st...1612 days ago
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
...ous solutions, and statistical supports on ancestral and extant adjacencies are provided. DeCoSTAR supports the features of previously contributed tools that reconstruct ancestral ad...1597 days ago
ngs-bits - Short-read sequencing tools
Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources: Binaries for Linux/macOS From sources for Linux/macOS From sources for Windows1583 days ago
modelStudio: a package automates the explanation of machine learning predictive models
...ite. It combines R with D3.js to produce plots and descriptions for various local and global explanations. Tools for model exploration unite with tools for EDA (Exploratory Data Ana...1577 days ago
gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
...tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser. gapFi...1576 days ago
1567 days ago
3D de novo assembly (3D DNA) pipeline
For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see Genome Assembly Cookbook on http://aidenlab.org/assembl...1567 days ago
Sequanix: a dynamic graphical interface for Snakemake workflows
A Python library dedicated to NGS analysis (e.g., tools to visualise standard NGS formats). A set of pip...ake framework) with more than 80 re-usable rules (see Rules). Original tools to help in the creation of su...1557 days ago
SeqMule: Automated human exome/genome variants detection
SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file.1551 days ago