Genome assembly forensics: finding the elusive mis-assembly
...e assemblies, and highlight several assembly errors in both draft and finished genomes. The software described is compatible with common assembly formats and is released, open-source,...1921 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
...e simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. All outputs can be written to standard file formats. A swift, versatile phylogen...1741 days ago
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Nucleus: Python and C++ code for reading and writing genomics data.
Nucleus is a library of Python and C++ code designed to make it easy to read, write and analyze data in common genomics file formats like SAM and VCF. In addition, Nucleus enables pai...1549 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 pipelines dedicated to NGS in the form of Snakefiles (Makefile-like with Python...1540 days ago
pbmm2:A minimap2 frontend for PacBio native data formats
pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output...1534 days ago
Best Practices for Variant Calling with the GATK
...as version 3.3. Genome Analysis Toolkit 03/19/15 Introduction to High-Throughput Sequencing data formats and methods Joel Thibault P...1530 days ago
SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.
...nd the target chromosomes that need to be mapped. Users also have option to download the generated visualizations in publication ready SVG or PNG formats.1431 days ago
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
...l implemented in DESeq2 [Love 2014].SHAMAN is compatible with standard formats for metagenomic analysis (.csv, .tsv, .biom) and figures can be downloaded in several formats. A presentation about SHAMAN...1353 days ago