Data management Tools

Genomepy is designed to provide a simple and straightforward way to download and use genomic data. This includes (1) searching available data, (2) showing the available metadata, (3) automatically downloading, preprocessing and matching data and (4) generating optional aligner indexes. All with sensible, yet controllable defaults. Currently, genomepy supports Ensembl, UCSC, NCBI and GENCODE.

The main purpose of HTSlib is to provide access to genomic information files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF and BCF formats). The library also provides interfaces to access and index genome reference data in FASTA format and tab-delimited files with genomic coordinates. It is utilized and incorporated into both SAMtools and BCFtools.

KentUtils is a collection of UCSC command-line bioinformatic utilities for genome browser data processing, including tools for format conversion, genome annotation, sequence analysis, and manipulation of genomic data formats such as BED, BigWig, BigBed, and BAM files.

Toolbox that allows you to filter and manipulate annotated vcf files.

API and command line utilities for the manipulation of VCF files.

BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.

Bamutil provides a serie of programs to work on SAM/BAM files.

Visualisation, quality control and taxonomic partitioning of genome datasets.

Python package for working with GFF and GTF files. It allows operations which would be complicated or time-consuming using a text-file-only approach.