Software Updates

PyMOL Open Source

open source version of the widely used molecular visualization package developed by Warren DeLano.

regtools

is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.

lorikeet

is a tool for digital spoligotyping of MTB strains from Illumina read data.

IMSEQ

(IMmunogenetic SEQuence Analysis) is a fast, PCR and sequencing error aware tool to analyze high throughput data from recombined T-cell receptor or immunoglobolin gene sequencing experiments. It derives immune repertoires from sequencing data in FASTA / FASTQ format.

Bloocoo

is a k-mer spectrum-based read error corrector, designed to correct large datasets with a very low memory footprint. It uses the disk streaming k-mer counting algorithm contained in the GATB library, and inserts solid k-mers in a bloom-filter. The correction procedure is similar to the Musket multistage approach. Bloocoo yields similar results while requiring far less memory: as an example, it can correct whole human genome re-sequencing reads at 70 x coverage with less than 4GB of memory.

Zerone

discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. After the job is done, Zerone checks the results and tells you whether it passes the quality control.

VarScan

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

Subread

comprises a suite of software programs for processing next-gen sequencing read data including

- Subread: a general-purpose read aligner which can align both genomic DNA-seq and RNA-seq reads. It can also be used to discover genomic mutations including short indels and structural variants.
- Subjunc: a read aligner developed for aligning RNA-seq reads and for the detection of exon-exon junctions. Gene fusion events can be detected as well.
- featureCounts: a software program developed for counting reads to genomic features such as genes, exons, promoters and genomic bins.
- Sublong: a long-read aligner that is designed based on seed-and-vote.
- exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.

VSEARCH

an alternative to the USEARCH tool developed by Robert C. Edgar (2010) for which the source code is not publicly available, VSEARCH is an open source, multithreaded 64-bit tool for processing and preparing metagenomics, genomics, and population genomics nucleotide sequence data. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling, and sorting. It also supports FASTQ file analysis, filtering, conversion, and merging of paired-end reads.

SpliceMap

is a de novo splice junction discovery and alignment tool. It offers high sensitivity and support for arbitrary RNA-seq read lengths.

CUDA

a tool that helps redistributable software libraries to support CUDA applications for Linux.

Cutadapt

finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

OpenMPI

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

MUSCLE

(multiple sequence comparison by log-expectation) a public domain multiple alignment software for protein and nucleotide sequences.

MPICH

a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.

MISO

a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.

MISO is installed as a standalone program and as a module within python.

ImageMagick

a software suite to create, edit, compose, or convert bitmap images.

ImageJ

a Java image processing program inspired by NIH Image that can display, edit, analyze, process, save and print 8-bit, 16-bit, and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw" and supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations can be performed in parallel with other operations.

HHsuite

an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

Ghostscript

an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.

Fiji

an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.

FASTA

a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.

EMBOSS

a program that integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

Clustal

a general purpose multiple sequence alignment program for DNA or proteins.

breseq

a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads.

CellProfiler

a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

breseq

a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads.

BLAST

(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.

OpenJDK

(Open Java Development Kit) a free and open source implementation of the Java Platform, Standard Edition (Java SE).

GCTA

(Genome-wide Complex Trait Analysis) a tool for genome-wide complex trait analysis with five main functions: data management, estimation of the genetic relationships from SNPs, mixed linear model analysis of variance explained by the SNPs, estimation of the linkage disequilibrium structure, and GWAS simulation. GCTA estimates the variance explained by all the SNPs on a chromosome or on the whole genome for a complex trait rather than testing the association of any particular SNP to the trait.

Fiji

an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.

FastQ Screen

allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

Cufflinks

a reference-guided assembler that assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

CUDA

a tool that helps redistributable software libraries to support CUDA applications for Linux.

Centrifuge

is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (e.g., 4.3 GB for ~4,100 bacterial genomes) yet provides very fast classification speed, allowing it to process a typical DNA sequencing run within an hour. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers.