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.
Allows users to interact with high-throughput sequencing data. SAMtools permits the manipulation of alignments in the SAM/BAM/CRAM formats: reading, writing, editing, indexing, viewing and converting SAM/BAM/CRAM format. It limits the mapping quality of reads with excessive mismatches and applies base alignment quality to fix alignment errors. This tool can sort and merge alignments, remove polymerase chain reaction (PCR) duplicates or generate per-position information.
Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and able to support projects of any size. The application compiles an assortment of command line allowing one to analyze of high-throughput sequencing (HTS) data in various formats such as SAM, BAM, CRAM or VCF. The website includes multiple documentation for guiding users.
A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information). The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ and many many others.
Provides a set of tools for biological computation written in Python. Biopython contains modules for reading and writing different sequence files formats and multiple sequence alignments, interacting with common tools (such as BLAST, ClustalW and EMBOSS), accessing key online databases, handling with 3D macro molecular structures and furnishing numerical methods for statistical learning. The main goal of this platform is to facilitate the use of Python for bioinformatics by generating reusable modules and classes.
Allows users to prepare sequence alignment/map files for variant calling in sequencing pipelines. elPrep is designed to run in memory, avoiding repeated file input/output between the preparation steps and merging their computations. Moreover, it can be used as a plugin for the Halvade MapReduce framework for executing sequencing pipelines in parallel on a cluster.