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://aidenla...1631 days ago
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memor...1628 days ago
Musket - a multistage k-mer spectrum based corrector
Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-me...1628 days ago
1626 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-li...1621 days ago
CLARK: Fast, accurate and versatile sequence classification system
CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the articl...1618 days ago
1616 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.1615 days ago
BlobToolKit: A toolkit for genome assembly QC
Filtering raw genomic datasets is essential to avoid chimeric assemblies and to increase the validity of sequence-based biological inference. BlobToolKit extends the Blo...1612 days ago
Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad&r...1611 days ago