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 article fo...1602 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.1599 days ago
LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call...1599 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 se...been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence...1599 days ago
BlobToolKit: A toolkit for genome assembly QC
...essential to avoid chimeric assemblies and to increase the validity of sequence-based biological inference. B.... BlobTools2 is a command-line program to convert assemblies and analysis results into datasets that ca...1596 days ago
Juicebox: Visualization and analysis software for Hi-C data
Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juic...1596 days ago
Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 2015 G...kshop, the current version of Broad’s Genome Analysis Toolkit (GATK) was version 3.3. Genome Analysis Toolkit...1595 days ago
ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis
ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data....nt-Derived Xenografts (PDXs) or host-pathogen interactions. Reference protein sequence...1570 days ago
1520 days ago
Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
Dahak is a software suite that integrates state-of-the-art open source tools for metag.... Tools in the dahak software suite will perform various steps in metagenomic analysis workflows including data pre-...1548 days ago