Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have pr...1603 days ago
iSeqQC: a tool for expression-based quality control in RNA sequencing
iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC...1597 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 vari...or 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...1595 days ago
Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 2015 GATK Workshop, part of the Br...Toolkit 03/19/15 Introduction to High-Throughput Sequencing data formats and methods Joe...1591 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...1574 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 serv...published code. We provided trained models for various depth of low-coverage sequencing Hi-C data. The depth of input...1581 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...1568 days ago
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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 accura...1519 days ago