Cyvcf2 is a Cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.

SAIGE is a package for efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks (SAIGE-GENE+).

Cell2cell is a Python library for cell communication analysis. This is a method to calculate, visualize and analyze communication between cell types. Cell2cell is suitable for single-cell RNA sequencing (scRNA-seq) data.

A streamgraph is a type of stacked area chart. It represents the evolution of a numeric variable for several groups. Areas are usually displayed around a central axis, and edges are rounded to give a flowing shape. This package provides an htmlwidget for building streamgraph visualizations.

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This package provides command line tools using the Bio++ library.

Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

DIAMOND is a BLAST-compatible local aligner for mapping protein and translated DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings.

Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and a command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.

randfold computes the probability that, for a given sequence, the Minimum Free Energy (MFE) of the secondary structure is different from MFE computed with random sequences.

This is a package that lets you process UMI-4C data from scratch to produce nice plots.

This package has been developed under ROpenSci gudelines to integrate conventional and cutting edge cytometry analysis tools under a unified framework. It aims to represent an intuitive and interactive approach to analysing cytometry data in R.

MoFax is a Python package for transcription factor motif analysis. It provides convenience functions to load and visualize factor models trained with MOFA+ in Python.

PDBFixer is designed to rectify issues in Protein Data Bank files. Its intuitive interface simplifies the process of resolving problems encountered in PDB files prior to simulation tasks.

This package provides a toolkit for measuring and comparing ATAC-seq results. It was written to make it easier to spot differences that might be caused by ATAC-seq library prep or sequencing. The main program, ataqv, examines aligned reads and reports some basic metrics.

This package provides several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable called bam.

Bowtie 2 is a fast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

Isolator analyzes RNA-Seq experiments. Isolator has a particular focus on producing stable, consistent estimates. It implements a full hierarchical Bayesian model of an entire RNA-Seq experiment. It saves all the samples generated by the sampler, which can be processed to compute posterior probabilities for arbitrarily complex questions, far beyond the confines of pairwise tests. It aggressively corrects for technical effects, such as random priming bias, GC-bias, 3' bias, and fragmentation effects. Compared to other MCMC approaches, it is exceedingly efficient, though generally slower than modern maximum likelihood approaches.

The package reads phylogenetic data in the phyloXML format. It also includes functions for writing data in this format.

Ngs-bits (Next-Generation Sequencing) is collection of short-read and long-read sequencing tools for diagnostics.

Taxtastic is software written in python used to build and maintain reference packages i.e. collections of reference trees, reference alignments, profiles, and associated taxonomic information.

This package provides tools for handling BAM, SAM, Tabix, bgzf, CRAM, CSIv1, CSIv2 and FAI files.

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from high-throughput sequencing reads.

Telomerecat is a tool for estimating the average telomere length (TL) for a paired end, whole genome sequencing (WGS) sample.

Telomerecat is adaptable, accurate and fast. The algorithm accounts for sequencing amplification artifacts, anneouploidy (common in cancer samples) and noise generated by WGS. For a high coverage WGS BAM file of around 100GB telomerecat can produce an estimate in ~1 hour.