MiTools: yet another Next Generation Sequencing (NGS) data processing tool (based on MiLib)
Using Homebrew on Mac OS X or Linux (linuxbrew)
brew tap milaboratory/all
brew install mitools
or just
brew install milaboratory/all/mitools
to upgrade already installed MiTools to the newest version:
brew update
brew upgrade mitools
- download latest MiTools version from release page
- unzip the archive
- add resulting folder to your
PATHvariable- or add symbolic link for
mitoolsscript to yourbinfolder - or use MiTools directly by specifying full path to the executable script
- or add symbolic link for
- Any OS with Java support (Linux, Windows, Mac OS X, etc..)
- Java 1.7 or higher
Cutting input fastq file to specified read length:
mitools cut -l 50 input.fastq.gz output.fastq.gz
Reverse-complement all reads:
mitools rc input.fastq.gz output.fastq.gz
Merge-overlap paired-end reads (like PEAR but works better in our experience; fast - based on bitap algorithm):
mitools merge input_R1.fastq.gz input_R2.fastq.gz output.fastq.gz
Split input file into chunks of 1M reads:
mitools split -c 1000000 input.fastq.gz output_{P}.fastq.gz
will produce output_0.fastq.gz, output_1.fastq.gz, ... files.
See mitools -h for available command paramenters and other useful actions.
See output of
mitools -h
for available actions.
Copyright 2016 MiLaboratory.com
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.