indelfixer

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A sensitive aligner for 454, Illumina and PacBio data, employing a full Smith-Waterman alignment against a reference.

Home https://github.com/cbg-ethz/InDelFixer
Versions 1.1
License GNU General Public License v3.0
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/indelfixer

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install indelfixer

and update with:

conda update indelfixer

Notes

InDelFixer is Java program that comes with a custom wrapper shell script. This shell wrapper is called “InDelFixer” and is on $PATH by default. By default “-Xms512m -Xmx1g” is set in the wrapper. If you want to overwrite it you can specify these values directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with “InDelFixer -Xms512m -Xmx1G”

docker

A Docker container is available at https://quay.io/repository/biocontainers/indelfixer.