This is a Perl interface to the HTS library for DNA sequencing.

Samtools implements various utilities for post-processing nucleotide sequence alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.

This package provides several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable called bam.

Blasr is a genomic sequence aligner for processing PacBio long reads.

This is package for including transposable elements in differential enrichment analysis of sequencing datasets. TEtranscripts and TEcount take RNA-seq (and similar data) and annotates reads to both genes and transposable elements. TEtranscripts then performs differential analysis using DESeq2. Note that TEtranscripts and TEcount rely on specially curated GTF files, which are not included due to their size.

This package provides the ASCAT R package that can be used to infer tumour purity, ploidy and allele-specific copy number profiles.

The package reads phylogenetic data in the phyloXML format. It also includes functions for writing data in this format.

CodingQuarry is a highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts.

This package provides R miscellaneous utilities for basic data manipulation, debugging, visualization, lsf management, and common mskilab tasks.

This package implements scalable gene regulatory network inference using tree-based ensemble regressors.

This package provides an implementation of chunked, compressed, N-dimensional arrays for R, Zarr specification version 2 (2024) <doi:10.5281/zenodo.11320255>.

SNAP is a fast and accurate aligner for short DNA reads. It is optimized for modern read lengths of 100 bases or higher, and takes advantage of these reads to align data quickly through a hash-based indexing scheme.

This package implements bindings for zarr store that are compatible with Bioconductor S4 data structures, namely the DataFrame and DelayedArray. This allows Zarr-backed data to be easily used as data frames with arbitrary sets of columns.

This package is a Python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. The mgatk package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.

This package provides Python bindings for lib2bit to access 2bit files with Python.

This package is designed to pileup the expressed alleles in single-cell or bulk RNA-seq data, which can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with other packages, which assigns cells to donors and detects doublets as vireo, even without genotyping reference.

This package is the C version of the deprecated cellSNP implemented in Python. Compared to cellSNP, this package is more efficient with higher speed and less memory usage.

inStrain is a Python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification.

Parabam is a tool for processing sequencing files in parallel. It uses Python's native multiprocessing framework to apply a user defined rule on an input file.

PyLiftover is a library for quick and easy conversion of genomic (point) coordinates between different assemblies.

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.

The Maxprobes package collects cross-reactive probes of Illumina methylation array 450K and EPIC/850K.

MethylDackel will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.

The WiggleTools package allows genomewide data files to be manipulated as numerical functions, equipped with all the standard functional analysis operators (sum, product, product by a scalar, comparators), and derived statistics (mean, median, variance, stddev, t-test, Wilcoxon's rank sum test, etc).

MACS is an implementation of a ChIP-Seq analysis algorithm for identifying transcript factor binding sites named Model-based Analysis of ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and it improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.