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 convol...n. Unlike other demultiplexers (e.g. Albacore and P...squiggle) which gives it greater sensitivity and fewer unclassified reads....1605 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 l...l approaches including unsupervised clustering, agglomerative hierarchical clustering and correl...1598 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 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 Works...5 Introduction to High-Throughput Sequencing data formats and methods Joel Thibault PDF...03/19/15 Mapping, processing, and d...deo 03/19/15 Variant calling and joint genotyping Sheila Chandran P...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...Assembler) by Jared Simpson, and BWA-MEM by Heng Li....parsed to identify variants. Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read su...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...published code. We provided trained models for various depth of low-coverage sequencing Hi-C data. The depth of input...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...1569 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 ac...blers. Furthermore, the generated assemblies in terms of contiguity and accuracy are on par with the other t...1521 days ago