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This package contains functions to extract information from Oxford Nanopore sequencing data and alignments.
Primer3 is a widely used program for designing PCR primers. PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.
This packages provides a collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.
This package provides a tool to extract assembly statistics from FASTA and FASTQ files.
This package contains the following programs: bamcollate2, bammarkduplicates, bammaskflags, bamrecompress, bamsort, bamtofastq.
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.
CMAPLE is a C++ reimplementation of MAPLE - a novel likelihood-based phylogenetic inference method for pandemic-scale epidemiological genomic data.
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.
SPAdes is an assembly toolkit containing various assembly pipelines.
This package provides a subset of the Regulatory Sequence Analysis Tools (RSAT).
This package provides an implementation of the CaVEMan program. It uses an expectation maximisation approach to calling single base substitutions in paired data. It is designed for use with a compute cluster. Most steps in the program make use of an index parameter. The split step is designed to divide the genome into chunks of adjustable size to optimise for runtime/memory usage requirements.
This package provides a phylogeny dating method using least-squares algorithms and criteria.
This package provides a new way of computing bootstrap supports in large phylogenies.
This package contains a few simple math function for other Oxford Nanopore processing scripts.
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.
Build contrasts for models defined with formulaic.
This package provides a tool to download or view data in the cloud environments of ICGC.
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.
This module provides code coverage metrics for Perl. Code coverage metrics describe how thoroughly tests exercise code. By using Devel::Cover you can discover areas of code not exercised by your tests and determine which tests to create to increase coverage.