Metagenomic Assembly of Ancient DaMaged reads with Nextflow.

Introduction

MADMAN is an assembly pipeline for ancient DNA.

MADMAN performs intial pre-processing of input FASTQ files. It then performs metagenomic de novo assembly with one or multiple assemblers, runs assembly quality-control, and finally screens for potentially truly-ancient contigs through fitting of damage patterns to typical ancient DNA damage distributions.

It is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Quick Start

i. Install nextflow

ii. Install either Docker or Singularity for full pipeline reproducibility (please only use Conda as a last resort; see docs)

iii. Download the pipeline and test it on a minimal dataset with a single command

nextflow run maxibor/madman -profile test,<docker/singularity/conda/institute>

Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

iv. Start running your own analysis!

nextflow run maxibor/madman -profile <docker/singularity/conda/institute> --reads '*_R{1,2}.fastq.gz'

See usage docs for all of the available options when running the pipeline.

Documentation

The nf-core/madman pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation
2. Pipeline configuration
   • Local installation
   • Adding your own system config
   • Reference genomes
3. Running the pipeline
4. Output and how to interpret the results
5. Troubleshooting

Credits

nf-core/madman was originally written by Maxime Borry.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on Slack (you can join with this invite).

Citation

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
ReadCube: Full Access Link

Help

$ nextflow run maxibor/madman --help
N E X T F L O W  ~  version 20.04.1
Launching `./main.nf` [focused_mendel] - revision: 41525792de
WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE
----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/madman v1.0dev
----------------------------------------------------
MADMAN: Metagenomic Assembly of Ancient DaMaged reads with Nextflow
 Homepage: https://github.com/maxibor/madman
 Author: Maxime Borry <borry@shh.mpg.de>
=========================================
Usage:
The typical command for running the pipeline is as follows:
nextflow run maxibor/madman --reads '/path/to/paired_end_reads_*.{1,2}.fastq.gz'
Mandatory arguments:
  --reads                           Path to input data (must be surrounded with quotes)

Settings:
  --phred                           Specifies the fastq quality encoding (33 | 64). Default: 33
  --single_end                      To specify if reads are single-end. Default: false
  --modern                          To specify if data are modern. Default: false
  --adapter_list                    List of sequencing adapters to trim. Default: madman/assets/adapter_list.txt
  --complexity_filter_poly_g_min    Length of poly-g min for clipping to be performed. Default: 10
  --megahit                         Specify to run megahit. Default: true
  --metaspades                      Specify to run metaSPAdes. Default: false
  --biospades                       Specify to run BiosyntheticSPAdes. Default: false
  --minlen                          Minimum contig length (bp) to retain. Default:  300
  --minread                         Minimum number of reads aligned to contig to consider contig. Default: 1000
  --coverage                        Minimum depth coverage to consider contig. Default: 0.5
  --wlen                            Window length from 5' end of reads to consider for damage estimation. Default: 35
  --mindamage                       Minimum frequency of C to T damage on the first base of the 5' end of the read. Default: 0.2

Options:
  --results                         The output directory where the results will be saved. Default: ./results
  --help  --h                       Shows this help page

Workflow