Read quality assessment software tools | High-throughput sequencing data analysis

Furnishes functions to control quality for high throughput sequence data. FastQC aims to provide a simple manner to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which users can employ to obtain a quick impression of whether data has any problems of which users should be aware before doing any further analysis.

Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and metagenomics. The software enables to generate custom workflows, which can combine quality control steps, adapter trimming, read mapping, variant detection, and multiple filtering and annotation steps into a pipeline.

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).

Assists users with DNA sequence analysis. Sequencher is a graphical application that integrates the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data. It can generate unique data visualizations using customized plots and graphs that produces ready-to-print graphs. This model also includes an extensive Sanger analysis features.

Enables users to work with high-throughput sequencing data. HTSeq is a program that simplifies development of scripts for processing and analyzing high-throughput sequencing (HTS) data. It contains parsers for common file formats for a variety of types of input data and is suitable as a general platform for a diverse range of tasks.