Bioinformatics Resources on Rivanna

UVA research community has access to numerous bioinformatics software installed and ready-to-use on Rivanna. They are all available via the LMod module system. In addition,

Click here for a comprehensive list.


Popular Bioinformatics Software

Below are some popular tools and useful links for their documentation and usage:

Tool Version Description Useful Links
BEDTools 2.26.0 BEDTools utilities allow one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. Homepage
Tutorial
BLAST+ 2.7.1 BLAST+ is a suite of command-line tools that offers applications for BLAST search, BLAST database creation/examination, and sequence filtering. Web BLAST
Manual
BWA 0.7.17 BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM Homepage
Manual
Rivanna FAQs
Bowtie2 2.2.9 Bowtie2 is a memory-efficient tool for aligning short sequences to long reference genomes. Homepage
Manual
Rivanna FAQs
FastQC 0.11.5 FastQC is a Java application that generates a comprehensive quality control report for raw sequencing data. Homepage
Documentation
GATK 4.0.0.0 The Genome Analysis Toolkit provide tools for variant discovery. In addition to SNP and INDEL identification in germline DNA and RNAseq data, GATK tools include somatic short variant calling, as well as tackle copy number and structural variation. User Guide
Rivanna FAQs
Picard 2.1.1 Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. Homepage
Documentation
SAMTools 1.7 SAMTools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage
Manual
SPAdes 3.10.1 SPAdes provide pipelines for assembling genomes from Illumina and IonTorrent reads, as well as hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. It supports paired-end reads, mate-pairs and unpaired reads. Homepage
Manual
STAR 2.5.3a Spliced Transcripts Alignment to a Reference (STAR) is a RNA-seq aligner based on an algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. Homepage
vsearch 2.7.1 VSEARCH (stands for Vectorized Search) is a toolkit for nucleotide sequence analyses, including database search and clustering algorithms. It supports clustering, chimera detection, database searching, merging of paired-end reads, and other sequence manipulation tools. Homepage

Genomes on Rivanna

RC maintains a set of ready-to-use reference sequences and annotations for commonly analyzed organisms in a convenient, accessible location on Rivanna:

/project/genomes/

Majority of files have been downloaded from Illumina’s genomes repository (iGenomes), which contain assembly builds and corresponding annotations from Ensembl, NCBI and UCSC. Each genome directory contain index files of the whole genome for use with aligners like BWA and Bowtie2. In addition, STAR2 index files have been generated for each of Homo Sapiens (human) and Mus musculus (mouse) genomic builds.

Rivanna PATH for your genome of interest:

Organism Source Build Whole Genome Index Files BaseDirectory
FASTA BWA Bowtie2 STAR2
Arabidopsis thaliana Ensembl TAIR9
TAIR10
NCBI build9.1
TAIR10
Chlorocebus sabeus NCBI chlSab2
Danio rerio Ensembl GRCz10
UCSC danRer10
Drosophila melanogaster Ensembl BDGP6
NCBI build5.3
build5.41
UCSC dm6
Escherichia coli strain K12, DH10B Ensembl EB1
NCBI 2008-03-17
Escherichia coli strain K12, MG1655 NCBI 2001-10-15
Homo sapiens Ensembl GRCh37
NCBI GRCh38
UCSC hg19
hg38
Mus musculus NCBI GRCm38
UCSC mm9
mm10
Pan troglodytes Ensembl CHIMP2.1
CHIMP2.1.4
NCBI build3.1
UCSC panTro3
panTro4

Additional Support

We are continually extending our library of code templates for usage on Rivanna. If you wish to use a bioinformatics software for your project and would like to see a HowTo Use on Rivanna guide, create a topic on the UVA Research Computing discussion board.