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.

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 investigates and measure the quantity of single-cell RNA-seq data. BUStools is useful for the manipulation of BUS files. This kind of files schematizes pseudoalignments of reads from single-cell RNA-seq experiments. This tool can sort, merge and convert BUS files to a textual representation. It can provide statistics on barcodes, unique molecular identifiers (UMIs) and gene counts.

Groups several programs assisting users to work on SAM/BAM files. For using BamUtil, users have to download the libStatGen program.

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.