ngsutils - Tools for next-gen se

https://github.com/ngsutils/ngsutils

Run the bamutils, bedutils, fastqutils, or gtfutils scripts. These are the main driver scripts that setup the appropriate environment (loading pysam) and run the requested command.

For ease of use, it is recommended that you add bamutils, bedutils, fastqutils, and gtfutils to your $PATH.

Running bamutils without any arguments will return a list of commands available. Running bamutils command will give you the parameters required for that command (or bedutils, etc...)

General usage format:

bamutils command {options} filename

bedutils command {options} filename

fastqutils command {options} filename

gtfutils command {options} filename