Python-airr provides a library by the AIRR community to for describing, reporting, storing, and sharing adaptive immune receptor repertoire (AIRR) data, such as sequences of antibodies and T cell receptors (TCRs).

Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files.

SeqAn is a C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It contains algorithms and data structures for string representation and their manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.

deMULTIplex is an R package for analyzing single-cell RNA sequencing data generated with the MULTI-seq sample multiplexing method. The package includes software to

1. Convert raw MULTI-seq sample barcode library FASTQs into a sample barcode UMI count matrix, and

2. Classify cell barcodes into sample barcode groups.

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.

This package provides Shiny apps for interactive exploration of single-cell data.

PiGX ChIPseq is an analysis pipeline for preprocessing, peak calling and reporting for ChIP sequencing experiments. It is easy to use and produces high quality reports. The inputs are reads files from the sequencing experiment, and a configuration file which describes the experiment. In addition to quality control of the experiment, the pipeline enables to set up multiple peak calling analysis and allows the generation of a UCSC track hub in an easily configurable manner.

Maxent is a stand-alone Java application for modelling species geographic distributions.

This package provides a GFF/GTF file parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.

This is a Python package for the interactive visualization of bulk RNA-seq data. It provides a range of plotting functions and interactive tools to explore and analyze bulk RNA-seq data.

BioRuby comes with a comprehensive set of Ruby development tools and libraries for bioinformatics and molecular biology. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.

This is a package providing efficient operations for single cell ATAC-seq fragments and RNA counts matrices. It is interoperable with standard file formats, and introduces efficient bit-packed formats that allow large storage savings and increased read speeds.

CD-HIT is a program for clustering and comparing protein or nucleotide sequences. CD-HIT is designed to be fast and handle extremely large databases.

This package is designed to streamline scATAC analyses in R.

This package is a Python wrapper for Aaron Quinlan's BEDtools programs, which are widely used for genomic interval manipulation or "genome algebra". pybedtools extends BEDTools by offering feature-level manipulations from with Python.

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.

Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments.

Fastahack is a small application for indexing and extracting sequences and subsequences from FASTA files. The included library provides a FASTA reader and indexer that can be embedded into applications which would benefit from directly reading subsequences from FASTA files. The library automatically handles index file generation and use.

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.

Entrez Direct (EDirect) is a method for accessing the National Center for Biotechnology Information's (NCBI) set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a terminal. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions.

SCENIC (Single-cell regulatory network inference and clustering) is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

This package provides an implementation of the BITS (Binary Interval Search) algorithm, an approach to interval set intersection. It is especially suited for the comparison of diverse genomic datasets and the exploration of large datasets of genome intervals (e.g. genes, sequence alignments).

Aragorn identifies transfer RNA, mitochondrial RNA and transfer-messenger RNA from nucleotide sequences, based on homology to known tRNA consensus sequences and RNA structure. It also outputs the secondary structure of the predicted RNA.

The package is ideal for analyzing RNA structure and chemical probing data.