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An accurate GFF3/GTF lift over pipeline

Tools for fast and flexible genome assembly scaffolding and improvement

Full-Length Alternative Isoform analysis of RNA

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)

Graph realignment tools for structural variants

RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes

HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, a…

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer

Technology agnostic long read analysis pipeline for transcriptomes

Raw nanopore signal mapper that enables real-time targeted sequencing

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

Structural Variants Pipeline for Long Reads

Structural variant toolkit for VCFs

CORGi - COmplex Rearrangement analysis with Graph-search

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

Oxford Nanopore Technologies fast5 API software

A versatile pairwise aligner for genomic and spliced nucleotide sequences

A single molecule sequence assembler for genomes large and small.

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations