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Resources software - Bioinformatics
| Name | Version | Description | Topic | Availability | Target user |
|---|---|---|---|---|---|
| Alphafold | 2.2.0,2.3.0,2.1.1 |
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 |
| Cricetulus_griseus | 1.0 |
Cricetulus griseus (Chinese hamster) - RefSeq assembly 1.0 |
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 ( G100) 0.11.2 (MARCONI) |
A quality control tool for high throughput sequencing data |
Bioinformatics | GALILEO100, MARCONI | all |
| Fastq_utils | 0.25.1 |
validate and manipulate fastq files |
Bioinformatics | GALILEO100 | all |
| Freebayes | 1.3.4 (G100) 1.1.0 (MARCONI) |
Freebayes, a haplotype-based variant detector |
Bioinformatics | GALILEO100, MARCONI | all |
| Fsl | 6.0.5.1 |
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 |
| Get-homologues-est | 20210828 |
A versatile software 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 |
| ig_Bos_taurus | release 8 |
This module comprehend genomic data from Bos taurus (cow). Sequences, Indexes and Annotations of the genome are present. |
Bioinformatics | MARCONI | all |
| ig_homo_sapiens | hg38, hg19 |
Annotated Illumina/UCSC Human Genome 38 |
Bioinformatics | MARCONI | all |
| ig_Mus_musculus | mm10 |
Ready-To-Use Reference Sequences and Annotations provided by illumina |
Bioinformatics | 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) |
Statistical computing and graphics |
Bioinformatics, Engineering, Life Science, Maths Libraries | GALILEO100, MARCONI | 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 | 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 |