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

This package provides a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). It uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. It further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.

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.

Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm, which is used to generate consensus sequences. It supports three alignment modes: local (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap), and three gap modes: linear, affine and convex (piecewise affine).

This package provides an interface for the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This includes interfaces to blastn, blastp, blastx, and makeblastdb.

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.

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 contains a few simple math function for other Oxford Nanopore processing scripts.

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

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.

SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies.

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

This package is used to apply filtering on raw VCF calls generated using CaVEMan.

The io_lib from the Staden package is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. It supports various DNA sequence read formats, in particular SCF, ABI, ALF, CTF, ZTR, SFF and SRF.

Build contrasts for models defined with formulaic.

This package contains a set of common Perl utilities for generating consistent Vcf headers. It primarily exists to prevent code duplication between some other projects.

This package provides tools for rapid prokaryotic genome annotation.

This package provides in uncompressed version of the gnomAD structural variant sites.