An interval map structure that is optimized for low memory (each interval is represented by about 3 words + whatever the cargo is) and has semantics that are appropriate for genomic intervals (namely, intervals can overlap and queries will return all matches together). It also designed to be used in two phases: a construction phase + query phase).

dRep is a Python program for rapidly comparing large numbers of genomes. dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.

F-Seq is a software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome Browser.

The alignment module of BioJava provides an API that contains

• implementations of dynamic programming algorithms for sequence alignment;

• reading and writing of popular alignment file formats;

• a single-, or multi- threaded multiple sequence alignment algorithm.

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

Biopython is a set of tools for biological computation including parsers for bioinformatics files into Python data structures; interfaces to common bioinformatics programs; a standard sequence class and tools for performing common operations on them; code to perform data classification; code for dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.

NGS is a domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously.

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.

This package contains data used by pagoda2. The data within this package are the 3000 bone marrow cells used for vignettes.

Megahit is a fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.

This package provides a client for the OmniPath web service and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation nichenetr.

This is a package for normalizing Hi-C contact counts efficiently.

ShoRAH is a project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools provide error correction, haplotype reconstruction and estimation of the frequency of the different genetic variants present in a mixed sample.

PAIRADISE is a method for detecting allele-specific alternative splicing (ASAS) from RNA-seq data. Unlike conventional approaches that detect ASAS events one sample at a time, PAIRADISE aggregates ASAS signals across multiple individuals in a population. By treating the two alleles of an individual as paired, and multiple individuals sharing a heterozygous SNP as replicates, PAIRADISE formulates ASAS detection as a statistical problem for identifying differential alternative splicing from RNA-seq data with paired replicates.

NanoSV is a software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.

This package provides procedures for efficient pythonic random access to fasta subsequences.

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+).

Fluff is a Python package that contains several scripts to produce pretty, publication-quality figures for next-generation sequencing experiments.

JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq, ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak boundaries accurately. JAMM is applicable to both broad and narrow datasets.

Segemehl is software to map short sequencer reads to reference genomes. Segemehl implements a matching strategy based on enhanced suffix arrays (ESA). It accepts fasta and fastq queries (gzip'ed and bgzip'ed). In addition to the alignment of reads from standard DNA- and RNA-seq protocols, it also allows the mapping of bisulfite converted reads (Lister and Cokus) and implements a split read mapping strategy. The output of segemehl is a SAM or BAM formatted alignment file.

BWA-Meth works for single-end reads and for paired-end reads from the directional protocol (most common). It uses the method employed by methylcoder and Bismark of in silico conversion of all C's to T's in both reference and reads. It recovers the original read (needed to tabulate methylation) by attaching it as a comment which BWA appends as a tag to the read. It performs favorably to existing aligners gauged by number of on and off-target reads for a capture method that targets CpG-rich region.

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 aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot: bigwig, bed (many options), bedgraph, links (represented as arcs), and Hi-C matrices. pyGenomeTracks can make plots with or without Hi-C data.

Kraken is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences. Kraken examines the k-mers within a query sequence and uses the information within those k-mers to query a database. That database maps k-mers to the lowest common ancestor (LCA) of all genomes known to contain a given k-mer.