Taxtastic is software written in python used to build and maintain reference packages i.e. collections of reference trees, reference alignments, profiles, and associated taxonomic information.

This is a drop-in replacement for the IlluminaHumanMethylationEPIC package. It utilizes a Manifest based on 1.0B5 annotation. As of version 0.3.0, the IlluminaHumanMethylationEPIC package still employs the 1.0B2 annotation manifest. A corresponding annotation package, IlluminaHumanMethylationEPICanno.ilm10b5.hg38, is available to ensure proper annotation. The decision to maintain the same name is due to complications in downstream processing caused by array name lookup in certain preprocessing options.

PySnpTools is a library for reading and manipulating genetic data. It can, for example, efficiently read whole PLINK *.bed/bim/fam files or parts of those files. It can also efficiently manipulate ranges of integers using set operators such as union, intersection, and difference.

MOSAIK is a program for mapping second and third-generation sequencing reads to a reference genome. MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT.

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.

Pyahocorasick is a fast, memory-efficient library for multi-pattern string search. This means that you can find multiple key strings occurrences at once in some input text.

This package lets you read and write the PLINK BED format, simply and efficiently.

Grassroots DICOM (GDCM) is an implementation of the DICOM standard designed to be open source so that researchers may access clinical data directly. GDCM includes a file format definition and a network communications protocol, both of which should be extended to provide a full set of tools for a researcher or small medical imaging vendor to interface with an existing medical database.

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

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the jellyfish dump command, or queried for specific k-mers with jellyfish query.

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

The main functions of FastQC are:

• Import of data from BAM, SAM or FastQ files (any variant);

• Providing a quick overview to tell you in which areas there may be problems;

• Summary graphs and tables to quickly assess your data;

• Export of results to an HTML based permanent report;

• Offline operation to allow automated generation of reports without running the interactive application.

This package provides a robust, parallelized Python CLI for annotating three prime UTR.

This package is a rasterization preprocessing framework that aggregates cellular information into spatial pixels to reduce resource requirements for spatial omics data analysis. SEraster reduces the number of points in spatial omics datasets for downstream analysis through a process of rasterization where single cells gene expression or cell-type labels are aggregated into equally sized pixels based on a user-defined resolution. SEraster can be incorporated with other packages to conduct downstream analyses for spatial omics datasets, such as detecting spatially variable genes.

This package provides a tool for identifying and removing doublets in single-cell RNA-seq data.

python-gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations. The files are loaded into a SQLite database, allowing much more complex manipulation of hierarchical features (e.g., genes, transcripts, and exons) than is possible with plain-text methods alone.

PiGx is a collection of genomics pipelines. It includes the following pipelines:

• PiGx BSseq for raw fastq read data of bisulfite experiments

• PiGx RNAseq for RNAseq samples

• PiGx scRNAseq for single cell dropseq analysis

• PiGx ChIPseq for reads from ChIPseq experiments

All pipelines are easily configured with a simple sample sheet and a descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples.

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.

Several studies focus on the inference of developmental and response trajectories from single cell RNA-Seq (scRNA-Seq) data. A number of computational methods, often referred to as pseudo-time ordering, have been developed for this task. CRISPR has also been used to reconstruct lineage trees by inserting random mutations. The tbsp package implements an alternative method to detect significant, cell type specific sequence mutations from scRNA-Seq data.

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

Sailfish is a tool for genomic transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. All you need to run sailfish is a fasta file containing your reference transcripts and a (set of) fasta/fastq file(s) containing your reads.

The ccwl is a concise syntax to express CWL workflows. ccwl is a compiler to generate CWL workflows from concise descriptions in ccwl. It is implemented as an EDSL in the Scheme programming language.

This tool detects batch effects in high-dimensional data based on chi^2-test.

Implementation of the Smith-Waterman algorithm.

Ritornello is a ChIP-seq peak calling algorithm based on signal processing that can accurately call binding events without the need to do a pair total DNA input or IgG control sample. It has been tested for use with narrow binding events such as transcription factor ChIP-seq.