LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
LoFreq* (i.e. LoFreq version 2) is a fast and sensitive...for inferring SNVs and indels from next-generation sequencing data. It makes full use of ba...qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel a...1597 days ago
Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 2015 GATK Workshop, part of th...s Toolkit 03/19/15 Introduction to High-Throughput Sequencing data formats and methods Joe...1593 days ago
SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA u...to the reference with BWA-MEM and parsed to identify variants. Sequencing reads are then realigned to t...1575 days ago
DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution
DeepHiC is a GAN-based model for enhancing Hi-C data resolution. We developed this ser...ed trained models for various depth of low-coverage sequencing Hi-C data. The depth of input data is estimated by its distribution comparing with...1583 days ago
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Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies...1569 days ago
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QuartataWeb: user-friendly server developed for polypharmacological and chemogenomics analyses.
Data on protein-drug and protein-chemical interactions are rapidly accumulating in databases such as DrugBan...bserved interactions, while the lack of data for a given protein-drug/chemical pair does...1553 days ago
HASLR: a hybrid assembler which uses both second and third generation sequencing reads
HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate...1521 days ago
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools usefu...well as a structural variation caller for Illumina sequencing data. GRIDSS calls vari...enome-wide break-end assembly, split read, and read pair evidence.1507 days ago