This package provides a set of R functions to parse markdown and other generic helpers.

RSeQC provides a number of modules that can comprehensively evaluate high throughput sequence data, especially RNA-seq data. Some basic modules inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, etc.

This package provides Python bindings for spoa, a C++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences

This package is used for cell type identification in spatial transcriptomics. It also handles cell type-specific differential expression.

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

This package provides a set of functions to parse and open (search query) links to genomics related and other websites for R. Useful when you want to explore e.g.: the function of a set of differentially expressed genes.

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

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.

Scallop is a reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts.

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.

Splicekit is a modular platform for splicing analysis from short-read RNA-seq datasets. The platform also integrates pybio for genomic operations and scanRBP for RNA-protein binding studies. The whole analysis is self-contained (one single directory) and the platform is written in Python, in a modular way.

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

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.

CIRI-long is a package for circular RNA identification using long-read sequencing data.

Bandage is a program for visualising de novo assembly graphs. It allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. De novo assembly graphs contain not only assembled contigs but also the connections between those contigs, which were previously not easily accessible. Bandage visualises assembly graphs, with connections, using graph layout algorithms. Nodes in the drawn graph, which represent contigs, can be automatically labelled with their ID, length or depth. Users can interact with the graph by moving, labelling and colouring nodes. Sequence information can also be extracted directly from the graph viewer. By displaying connections between contigs, Bandage opens up new possibilities for analysing and improving de novo assemblies that are not possible by looking at contigs alone.

Sylamer is a system for finding significantly over or under-represented words in sequences according to a sorted gene list. Typically it is used to find significant enrichment or depletion of microRNA or siRNA seed sequences from microarray expression data. Sylamer is extremely fast and can be applied to genome-wide datasets with ease. Results are plotted in terms of a significance landscape plot. These plots show significance profiles for each word studied across the sorted genelist.

TSIS is used for detecting transcript isoform switches in time-series data. Transcript isoform switches occur when a pair of alternatively spliced isoforms reverse the order of their relative expression levels. TSIS characterizes the transcript switch by defining the isoform switch time-points for any pair of transcript isoforms within a gene. In addition, this tool describes the switch using five different features or metrics. Also it filters the results with user’s specifications and visualizes the results using different plots for the user to examine further details of the switches.

Newick-utils is a suite of utilities for processing phylogenetic trees in Newick format. Functions include re-rooting, extracting subtrees, trimming, pruning, condensing, drawing (ASCII graphics or SVG).

HTSJDK is an implementation of a unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing (HTS) data. There are also an number of useful utilities for manipulating HTS data.

Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools.

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.

VSEARCH supports DNA sequence searching, clustering, chimera detection, dereplication, pairwise alignment, shuffling, subsampling, sorting and masking. The tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch).

Savvy is the official C++ interface for the SAV file format and offers seamless support for BCF and VCF files.

wfmash is a DNA sequence read mapper based on mash distances and the wavefront alignment algorithm. It is a fork of MashMap that implements base-level alignment via the wflign tiled wavefront global alignment algorithm. It completes MashMap with a high-performance alignment module capable of computing base-level alignments for very large sequences.