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File editing software tools | High-throughput sequencing data analysis

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EMBOSS / European Molecular Biology Open Software Suite

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.

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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.

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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.

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Software

MolProp TK TAPAS MicrobiomeWorkflow

Users

pengjiang

Chinese Academy of Sciences

Ana Quezada

Laboratory of Molecular Biomedicine

zd Lee

Sichuan University

Databases

MEMA LOX-DB Orthonome

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