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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Permits to create, parse, edit and write graphical fragment assembly (GFA) files. GfaPy provides a complete interface to parse files in GFA, a format allowing for the description of generic sequence graphs. It can be modified to incorporate future changes in the GFA specification. It offers syntactic and semantic validation to guarantee valid GFA data. It can be used for GFA 1 and GFA 2 files.
Allows researchers to manipulate CSV and TSV files. csvtk is based on the utilization of shell commands and permits rapid data investigation. It can be implemented into analysis pipelines.
Groups several programs assisting users to work on SAM/BAM files. For using BamUtil, users have to download the libStatGen program.
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.
Offers to users several features to exploit genes and transcripts in general feature format (GFF) through the gene transfer format (GTF2) and GFF3 versions. GFF utilities provides a tool, gffread, for the validation, filtering and converting GFF files. gffcompare is another program that allows the evaluation and comparison of the accuracy of transcript assemblers and the intron/exon coordinates.
Provides a binary package to read raw signal data from FAST5 files. python-fast5 is a library for accessing Oxford Nanopore Technologies sequencing data. It includes a read-write access to fast5 files and a Python wrapper that enables read-only access to fast5 files.
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