Mapping

Mapping is one of the major functions of NGLess. Here we describe, in more detail, some of its functionality.

Mapping is implemented using bwa. As of version 1.4, NGLess uses bwa 0.7.17 by default.

By default, bwa is called with default parameters. If the mode_all argument is set to true, then -a is passed to bwa.

Low memory mode

As databases get very large, memory requirements can grow very large. In order to make large databases accessible to users without access to large memory machines, NGLess implements a simple heuristic: it splits the input database into smaller blocks, processes each one in turn and combines the results at the end.

To enable low-memory mode, use the block_size_megabases in the script. Set it to a value that is less than the available memory. Note that this does change the results (although the impact is limited).

A FAQ is why the memory requirements are not a configuration option and must be specified in the script. As low memory mode is heuristic, it can potentially change results. As NGLess aims to capture all parameters that can change the result inside the script, it must be specified as an argument to map().

Using SOAPAligner

Note

Support for SOAPAligner is experimental (as of version 0.6)

You can use SOAPAligner as an alternative to bwa using the following code:

import "soap" version "0.0"

input = ....

mapped = map(input, mapper="soap")

Note that, unlike the case for bwa, SOAPAligner is not bundled with NGLess and must be in the PATH to be used.