File editing software tools | High-throughput sequencing data analysis

Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.

Provides functions for the import-export of some standard systems biology file formats and a set of algorithms to analyze and reduce the complexity of biological networks. BiNoM provides the user with a complete interface for the analysis of biological networks in Cytoscape environment.

Provides a bioinformatics library written in the D programming language. BioD allows to benefit of automatic parallelization of tasks when it’s possible for example reading and write on BAM files. This software curtains the garbage collection (GC) overhead by avoiding unnecessary memory allocations. It also offers support for handling common biological data formats.

Provides string containers, string matching algorithms, and utilities for manipulating large biological sequences or sets of sequences. Biostrings is an R package that uses (1) R external pointers to store the string data, (2) bit patterns to encode the string data, and (3) provides users with a class of objects where each instance can store a set of views on the same big string.

Reads and writes high-throughput sequencing data. The htsfile utility attempts to identify what kind of high-throughput sequencing data files the specified files are, and provides minimal viewing capabilities for some kinds of data file. It can identify sequencing data files such as SAM, BAM, and CRAM; variant calling data files such as VCF and BCF; index files used to index these data files; and compressed versions of many of them.