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Resources software - Bioinformatics

Name Version Description Topic Availability Target user
Alphafold 2.2.0

AI system that predicts a protein's 3D structure from its amino acid sequence.

Bioinformatics GALILEO100 restricted
Annovar 2016Feb01 (MARCONI), 2019Oct24 (G100)

A software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).

Bioinformatics GALILEO100, MARCONI all
Ataqv 1.0.0

Ataqv is a toolkit for measuring and comparing ATAC-seq resultsand to make it easier to spot differences that might be caused by library prep or sequencing.

Bioinformatics MARCONI all
BBMap 37.87

This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded.

Bioinformatics MARCONI all
Bcftools 1.13 (G100), 1.2 (MARCONI)

BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF

Bioinformatics GALILEO100, MARCONI all
Beagle 4.1

 Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.

Bioinformatics MARCONI all
Bedtools 2.30.0(G100) 2.26(Bedtools2Marconi)

A toolset for genome arithmetic.

Bioinformatics GALILEO100, MARCONI all
BLAST+ 2.12.0

Basic Local Alignment Search Tool

Bioinformatics GALILEO100 all
Blat 36

Blat is an alignmet tool for proteic and genomic sequences

Bioinformatics MARCONI all
Bowtie 1.1.2 (MARCONI) 1.3.0 (G100)

Bowtie is an ultrafast, memory-efficient short read aligner.

Bioinformatics GALILEO100, MARCONI all
Bowtie2 2.4.4 (G100) 2.2.9 (Marconi)

Fast and sensitive read alignment

Bioinformatics GALILEO100, MARCONI all
Bwa 0.7.12 (G100) 0.7.15 (MARCONI)

Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping.

Bioinformatics GALILEO100, MARCONI all
Cactus 2.1.1

Cactus is a reference-free whole-genome multiple alignment program

Bioinformatics GALILEO100 all
Chimera 1.12 (MARCONI) 1.15 (G100)

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures

Bioinformatics, Chemistry, Physics, Visualisation GALILEO100, MARCONI all
ChromHMM 1.14

ChromHMM is software for learning and characterizing chromatin states.

Bioinformatics MARCONI all
Cufflinks 2.2.1

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

Bioinformatics GALILEO100 academic
Deeptools 2.0

Tools for exploring deep sequencing data

Bioinformatics MARCONI all
Dfast 1.2.12

DFAST is a flexible and customizable pipeline for prokaryotic genome annotation as well as data submission to the INSDC

Bioinformatics GALILEO100 all
Dwgsim 0.1.14

Genome simulation 

Bioinformatics GALILEO100 all
Ericscript 0.5.5

EricScript is a computational framework for the discovery of gene fusions in paired end RNA-seq data.

Bioinformatics MARCONI all
Fastqc 0.11.9 (M100, G100) 0.11.2 (MARCONI)

 A quality control tool for high throughput sequencing data

Bioinformatics GALILEO100, MARCONI, MARCONI100 all
Freebayes 1.3.4 (G100) 1.1.0 (MARCONI)

Freebayes, a haplotype-based variant detector

Bioinformatics GALILEO100, MARCONI all

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Bioinformatics, Life Science GALILEO100 academic
FusionCatcher 0.99.6a

Finder of somatic fusion-genes in RNA-seq data.

Bioinformatics MARCONI all
GATK 4.0(MARCONI) 4.2.0 (G100)

GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data.

Bioinformatics, Life Science GALILEO100, MARCONI academic
Gcta 1.94.1

Software package to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait and for other analyses of data from genome-wide association studies (GWASs)

Bioinformatics GALILEO100 academic
Get-homologues-est 20210828

A package for pan-genome analysis

Bioinformatics GALILEO100 all
HISAT2 2.0.4 (MARCONI) 2.2.1 (G100)

Graph-based alignment of next generation sequencing reads to a population of genomes

Bioinformatics GALILEO100, MARCONI all
Jellyfish 2.3.0

A fast multi-threaded k-mer counter

Bioinformatics GALILEO100 all
Kraken 2

Kraken is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences.

Bioinformatics GALILEO100 all
Macs 2.1.0

Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq)

Bioinformatics MARCONI all
Nest 3.3

NEST is a simulator for spiking neural network models focusing on the dynamics, size and structure of neural systems.

Bioinformatics GALILEO100 all
NucleoATAC 0.2.1

NucleoATAC is a python package for calling nucleosome positions and occupancy using ATAC-Seq data.

Bioinformatics MARCONI all
Picard 2.25.7 (G100), 2.7.1 (Marconi)

Utilities for manipulating SAM files

Bioinformatics GALILEO100, MARCONI all
PLINK 1.90

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Bioinformatics GALILEO100 academic
R 4.2.0 (G100) 3.6.1 (Marconi) 4.0.1 (M100)

Statistical computing and graphics

Bioinformatics, Engineering, Life Science, Maths Libraries GALILEO100, MARCONI, MARCONI100 all
Rsem 1.3.0 (Marconi)

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data

Bioinformatics MARCONI all
Salmon 1.5.1

Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Bioinformatics GALILEO100 all
Sambamba 0.6.6

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files.

Bioinformatics MARCONI all
Samtools 1.3.1(Marconi)1.13(G100)

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Bioinformatics GALILEO100, MARCONI all
Seqtk 1.2-r94 (Marconi)

A tool for processing sequences in FASTA or FASTQ format.

Bioinformatics MARCONI all
Snpeff 4.3k

SnpEff is a toolthat annotates and predicts the effects of variants on genes (such as amino acid changes).

Bioinformatics MARCONI all
Sra 3.0.0(Galileo100) 2.8.1 (Marconi)

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archive and download them locally

Bioinformatics, Life Science GALILEO100, MARCONI all
Star 2.7.9a (G100) 2.5.2a(Marconi)

Spliced Transcripts Alignment to a Reference

Bioinformatics GALILEO100, MARCONI all
Stringtie 2.1.6(G100) 1.3.1 (Marconi)

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.

Bioinformatics GALILEO100, MARCONI all
Tabix 0.2.6

Generic indexer for TAB-delimited genome position files.

Bioinformatics GALILEO100 all
Tophat 2.1.1 (G100) 2.0.12 (Marconi)

A spliced read mapper for RNA-Seq

Bioinformatics GALILEO100 all
Trimmomatic 0.39

A flexible read trimming tool for Illumina NGS data

Bioinformatics, Life Science GALILEO100, MARCONI, MARCONI100 all
Usearch 11.0.667

USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST

Bioinformatics GALILEO100 academic
Varscan 2.4.2 (G100, Marconi)

VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments.

Bioinformatics, Life Science GALILEO100, MARCONI all
Vcftools 0.1.16

VCFtools is a program package designed for working with VCF files.

Bioinformatics GALILEO100 all
Vep 104

Variant Effect Predictor

Bioinformatics GALILEO100 all