Tool for the Quality Control of Long-Read Defined Transcriptomes

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ClairS-TO - a deep-learning method for tumor-only somatic variant calling

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtool…

Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/

A package to run real time analysis of nanopore methylation data.

Tools (written in C using htslib) for manipulating next-generation sequencing data

HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

Identification of differential RNA modifications from nanopore direct RNA sequencing

A comprehensive cancer DNA/RNA analysis and reporting pipeline

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Nanopore demultiplexing, QC and alignment pipeline

Plot structural variant signals from many BAMs and CRAMs

RF model and functions to estimate tumor purity using methylation data

Minotour API, web and client code

🦀 Small exercises to get you used to reading and writing Rust code!

Structural variant caller for real-time long-read sequencing data

A tool to detect structural variant

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Long read based human genomic structural variation detection with cuteSV

Structural variation caller using third generation sequencing

De novo assembly from Oxford Nanopore reads.

De novo assembler for single molecule sequencing reads using repeat graphs

A Transformer-based model for read-level DNA methylation pattern identification and tumour deconvolution

scripts used for Grabovska et al methylCIBERSORT analysis