Software Updates

gdcm

Grassroots DiCoM is a C++ library for DICOM medical files. It is accessible from Python, C#, Java and PHP.

igvtools

command line tools for IGV

p7zip

p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org ) for Unix.

plastid

Plastid is a Python library designed specifically for nucleotide-resolution analysis of genomics and NGS data.

ASCIIGenome

a command-line genome browser running from terminal window and solely based on ASCII characters.

DCMTK

DCMTK is a collection of libraries and applications implementing large parts the DICOM standard.

Wally

Plotting of aligned sequencing reads, assembled contigs or pan-genome graphs in BAM/CRAM/GFA format and visualization of genomic variants.

prodigal-gv

A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes.

gfastats

gfastats is a single fast and exhaustive tool for summary statistics and simultaneous fa (fasta, fastq, gfa [.gz]) genome assembly file manipulation. gfastats also allows seamless fasta<>fastq<>gfa[.gz] conversion. It has been tested in genomes even >100Gbp.

MDAnalysis

an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

AlphaFold

an implementation of the inference pipeline of AlphaFold using a completely new model that was entered in CASP14.

chopper

Rust implementation of NanoFilt+NanoLyse, both originally written in Python. This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file.

AmberTools

a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.