3D de novo assembly (3D DNA) pipeline
For a detailed description of the pipeline and how it int...with other tools designed by the Aiden Lab see Genome Assembly Cookbook on&nbs...ipeline and to reproduce the Hs2-HiC and the AaegL4 genomes reported in (Dudchenko...1617 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...that are used to estimate weak kmer count threshold, lower for more divergent genome (default: 0.95) -ek INT: ex...1615 days ago
Musket - a multistage k-mer spectrum based corrector
Musket is a well-established leading next-generation sequencing read error corr...Our performance evaluation results, in terms of correction quality and de novo genome assembly measures, reveal tha...1615 days ago
1612 days ago
Sequanix: a dynamic graphical interface for Snakemake workflows
A Python library dedicated to NGS analysis (e.g., tools to visualise standard NGS...ions: sequana_coverage ease the extraction of genomic regions of interest and genome coverage information sequana...1608 days ago
CLARK: Fast, accurate and versatile sequence classification system
CLARK, a method based on a supervised sequence classifica...ssification of metagenomic reads to known bacterial genomes, and (2) the assignment of B...he absence of a finished assembly for the reference genome), CLARK outperforms in classi...1605 days ago
1603 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.1602 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 Bl...1599 days ago
Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 2015...this workshop, the current version of Broad’s Genome Analysis Toolkit (GATK) was version 3.3. Genome Analysis Toolkit...1598 days ago