Snakemake pipeline to analyze retrotransposable element 'omics data.
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Updated
May 31, 2024 - R
Snakemake pipeline to analyze retrotransposable element 'omics data.
Nanomotif - a tool for identifying methylated motifs in metagenomic samples
A bioinformatics tool for working with modified bases
Automated data mangement for Oxford Nanopore DNA sequencing instruments
Anglerfish - Nanopore reads from Illumina libraries
😎 This repository contains scripts that I wrote for data analysis and visualization.
Biochemical-free targeting of RNA classes during direct RNA sequencing
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Assembly and binning of metagenomes
Simple bacterial assembly and annotation pipeline
SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data.
RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440)
Graph-based assembly phasing
Research release basecalling models and configurations
A PyTorch Basecaller for Oxford Nanopore Reads
Methylation/modified base calling separated from basecalling.
Evaluating Nanopore-based bacterial variant calling
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
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