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This package provides procedures to calculate statistics for Oxford Nanopore sequencing data and alignments.
This package provides in uncompressed version of the gnomAD structural variant sites.
CMAPLE is a C++ reimplementation of MAPLE - a novel likelihood-based phylogenetic inference method for pandemic-scale epidemiological genomic data.
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.
This packages provides a collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.
Bioparser is a C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.
This package provides a tool to extract assembly statistics from FASTA and FASTQ files.
This package provides a subset of the Regulatory Sequence Analysis Tools (RSAT).
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.
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 package contains a set of common Perl utilities for generating consistent Vcf headers. It primarily exists to prevent code duplication between some other projects.
Control-FREEC automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. The control (matched normal) sample is optional for whole genome sequencing data but mandatory for whole exome or targeted sequencing data. For whole genome sequencing data analysis, the program can also use mappability data (files created by GEM).
The Spliced Transcripts Alignment to a Reference (STAR) software is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.
Build contrasts for models defined with formulaic.
The CodeMin minimization library provides a set of lightweight minimization functions originally developed for the CodeAxe phylogenetic analysis package.
MCView creates a Shiny app facilitating interactive exploration and annotation of Metacell models.
Primer3-py is a Python-abstracted API for the popular Primer3 library. The intention is to provide a simple and reliable interface for automated oligo analysis and design.
Primer3-py also includes bindings for the Primer3 primer design engine if you’d prefer to use an established pipeline. The IO parameters mirror those of the original Primer3, but you don’t have to deal with messy and slow file IO for your automated workflows.