This package provides the reference implementation of CGP workflow for CaVEMan SNV analysis.

Primer3 is a widely used program for designing PCR primers. PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.

This package provides in uncompressed version of the gnomAD structural variant sites.

Mellon is a non-parametric cell-state density estimator based on a nearest-neighbors-distance distribution. It uses a sparse gaussian process to produce a differntiable density function that can be evaluated out of sample.

This package provides gzip-like compression for tskit tree sequences. Compression is lossless for supported tskit tree sequences.

This package provides an implementation of the CaVEMan program. It uses an expectation maximisation approach to calling single base substitutions in paired data. It is designed for use with a compute cluster. Most steps in the program make use of an index parameter. The split step is designed to divide the genome into chunks of adjustable size to optimise for runtime/memory usage requirements.

This package contains a few simple math function for other Oxford Nanopore processing scripts.

This package is used to apply filtering on raw VCF calls generated using CaVEMan.

This package provides a Cython helper library for pyranges for finding nearest intervals in linear time at C speed.

msprime is a population genetics simulator based on tskit. Msprime can simulate random ancestral histories for a sample of individuals (consistent with a given demographic model) under a range of different models and evolutionary processes. Msprime can also simulate mutations on a given ancestral history (which can be produced by msprime or other programs supporting tskit) under a variety of genome sequence evolution models.

This package provides tools for filtering on quality and/or read length, and optional trimming after passing filters. Reads from stdin, writes to stdout. Optionally reads directly from an uncompressed file specified on the command line. It is intended to be used directly after fastq extraction, prior to mapping, or in a stream between extraction and mapping.

bio2zarr efficiently converts common bioinformatics formats to Zarr format.

Tools:

• vcf2zarr converts VCF data to VCF Zarr format;

• plink2zarr converts PLINK 1.0 data to VCF Zarr format;

• tskit2zarr converts tskit data into VCF Zarr format;

• vcfpartition is a utility to split an input VCF into a given number of partitions;

• zipzarr is a utility for zipping/unzipping Zarr directory stores.

This packages provides a collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.

tstrait is a Python package to simulate quantitative traits from a given tree sequence.

This package provides tools for rapid prokaryotic genome annotation.

Vcztools provides a Python API to efficiently read VCZ data from local files and remote object stores using bcftools-compatible region and variant filtering syntax. It aims to provide a drop-in replacement for a subset of bcftools functionality.

IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data such as:

• Recombination model probability distribution

• Hypermutation model

• Best candidates recombination scenarios

• Generation probabilities of sequences (even hypermutated)

Its heavily object oriented and modular style was designed to ensure long term support and evolvability for new tasks in assessing TCR and BCR receptors features using modern parallel architectures.

This package provides a tool to download or view data in the cloud environments of ICGC.