Bioinformatics workflow tools | RNA sequencing data analysis

Assists users in manipulating high-throughput sequencing (HTS) data and formats. Picard is a Java toolkit that provides a set of command line scripts. It comprises Java-based utilities that manipulate SAM files, and a Java API for creating new programs that reads and writes SAM files. Both SAM text format and SAM binary (BAM) format are supported. It also works with next generation sequencing (NGS).

Offers an intuitive user interface and built-in workflows for a variety of genomic applications that guide researchers though every step of the analysis process. Partek Genomics Suite gives biologists, bioinformaticists, and statisticians a single, integrated solution for trustworthy results with a user-friendly interface, comprehensive workflows, and ability to support all next generation sequencing, microarray, and qPCR platforms.

Identifies differentially expressed genes from count data or previously normalized count data. NOISeq empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition. This reference distribution is then used to assess whether the M-D values computed between two conditions for a given gene are likely to be part of the noise or represent a true differential expression.

A comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads output by high-throughput sequencing technology (FASTQ, QSEQ, FASTA, SAM, or BAM files). Rockhopper supports the following tasks: reference based transcript assembly; de novo transcript assembly; normalizing data from different experiments; quantifying transcript abundance; testing for differential gene expression; characterizing operon structures; visualizing results in a genome browser.

Automates the process of genotyping microsatellite repeats in Huntington disease (HD) data. ScaleHD is a pipeline designed to be used for large-scale automated genotyping of HTT GAC/CCG repeat parallel sequencing data. It performs quality control, sequence alignment and genotyping on all file pairs presented by the user as input. The pipeline consists of three main stages: sequence quality control (SeqQC), sequence alignment (SeqALN) and automated genotyping (GType).