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

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.

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.

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets.

This package contains the following programs: bamcollate2, bammarkduplicates, bammaskflags, bamrecompress, bamsort, bamtofastq.

CAT and BAT are pipelines for the taxonomic classification of long DNA sequences and MAGs of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately.

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

The IQ-TREE software was created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid accumulation of phylogenomic data, leading to a need for efficient phylogenomic software that can handle a large amount of data and provide more complex models of sequence evolution. To this end, IQ-TREE can utilize multicore computers and distributed parallel computing to speed up the analysis. IQ-TREE automatically performs checkpointing to resume an interrupted analysis.

As input IQ-TREE accepts all common sequence alignment formats including PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable report file (name suffix .iqtree), a NEWICK tree file (.treefile) which can be visualized by tree viewer programs such as FigTree, Dendroscope or iTOL.

Key features of IQ-TREE:

• Fast and effective stochastic algorithm to reconstruct phylogenetic trees by maximum likelihood;

• An ultrafast bootstrap approximation (UFBoot) to assess branch supports;

• An ultrafast and automatic model selection (ModelFinder);

• A flexible simulator (AliSim) which can simulate sequence alignments under more realistic models than Seq-Gen and INDELible;

• Several fast branch tests like SH-aLRT and aBayes test and tree topology tests like the approximately unbiased (AU) test.

This package provides IQ-TREE version 2.

This package provides a tool to extract assembly statistics from FASTA and FASTQ files.

This package provides procedures to calculate statistics for Oxford Nanopore sequencing data and alignments.

Primer3-py is a Python-abstracted API for the popular Primer3 library. The intention is to provide a simple and reliable interface for automated oligo analysis and design.

Primer3-py also includes bindings for the Primer3 primer design engine if you’d prefer to use an established pipeline. The IO parameters mirror those of the original Primer3, but you don’t have to deal with messy and slow file IO for your automated workflows.

FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.

Biosoup is a C++ collection of header-only data structures used for storage and logging in bioinformatics tools.

This package provides a phylogeny dating method using least-squares algorithms and criteria.

The CodeMin minimization library provides a set of lightweight minimization functions originally developed for the CodeAxe phylogenetic analysis package.

CMAPLE is a C++ reimplementation of MAPLE - a novel likelihood-based phylogenetic inference method for pandemic-scale epidemiological genomic data.

MetaMaps is tool specifically developed for the analysis of long-read (PacBio/Oxford Nanopore) metagenomic datasets.

scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.

This package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenburg.