mitool consensus

Assemble consensuses for sequences inside tag groups.(ex. UMI-based correction)

Usage:

mitool consensus [OPTIONS] SOURCE DESTINATION

Arguments:

SOURCE

Input *.mic file

DESTINATION

Output *.mic file.

Options:

-g, --group-tag <TEXT>

Tags to build groups of reads for consensus assembly (e.g. CELL, UMI, etc...). If not set MiTool will use defaults if preset was specified on the parse step.

-a, --assemble-tag <TEXT>

Tags to assemble consensuses for (e.g. R1, R2, PAYLOAD, etc...). If not set MiTool will use defaults if preset was specified on the parse step.

--use-system-temp

Use system temp folder for temporary files

`-t, --threads

Number of processing threads

-r, --report <PATH>

Human readable report file. If file already exists, it will be overwritten.

-O <VALUE>

Override consensus assembly parameters.

-h, --help

Show this message and exit