1619 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&nbs...peline and to reproduce the Hs2-HiC and the AaegL4 genomes...1618 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)...that are used to estimate weak kmer count threshold, lower for more divergent genome...1615 days ago
Musket - a multistage k-mer spectrum based corrector
Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Ill...Our performance evaluation results, in terms of correction quality and de novo genome...1615 days ago
1613 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 d...ions: sequana_coverage ease the extraction of genomic regions of interest and genome...1608 days ago
CLARK: Fast, accurate and versatile sequence classification system
CLARK, a method based on a supervised sequence classification using discriminative ...sification of metagenomic reads to known bacterial genomes, and (2) the assignment of B...e absence of a finished assembly for the reference genome)...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