taco-read-filtering¶
This repository implements a read filtering workflow for dahak-taco.
In this documentation we will cover:
-
Download raw sequence data from OSF data store (wget).
-
Assess the quality of the pre-filtered reads (fastqc)
-
Trim and filter the reads based on a quality threshold (trimmomatic)
-
Assess the quality of the post-filtered reads (fastqc)
-
Interleave post-filtered reads (khmer)
We will not cover:
- How to install
taco - The basics of
taco
For those, see the dahak-taco documentation.
Setting Up Taco¶
To run these workflows, you must have taco installed.
See dahak-taco documentation
for installation instructions.
Once taco is installed, it will be available on the
command line. The taco commands covered in this document
should be run from the top-level directory of this repository
(this is true of any taco workflow repository).
What's In This Repository¶
Workflow files:
rules/- contains rule and workflow definitionsworkflow-config/- contains workflow configuration filesworkflow-params/- contains workflow parameter filesdocker/- contains custom Docker images for use in taco workflows
Documentation files:
docs/- contains the documentation files (i.e., the document you're reading now)mkdocs.yml- configuration file for mkdocs, the documentation generator used by this repomkdocs-material-dib/- git submodule containing mkdocs theme
Workflow¶
Read Filtering Workflow: Quickstart
Read Filtering Workflow: The Rules