sanger-tol/longreadmag

Introduction

sanger-tol/longreadmag is a bioinformatics pipeline for the assembly and binning of metagenomes using PacBio HiFi data and (optionally) Hi-C Illumina data.

1. Assembles raw reads using (metaMDBG)
2. Maps HiFi and (optionally) Hi-C reads to the assembly using minimap2 and bwa-mem2.
3. Bins the assembly using MetaBat2, MaxBin2, Bin3C (Hi-C binning), and Metator (Hi-C binning).
4. (optionally) refine the bins using DAS_Tool and MagScoT.
5. Assesses the completeness and contamination of bins using CheckM2 and assesses ncRNA content using tRNAscan-SE for tRNA and Infernal+Rfam for rRNA.
6. Assigns taxonomy to bins using GTDB-TK and converts assignments to NCBI taxonomy labels.
7. Summarises information at the bin level.

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a YAML with your input data that looks as follows:

input.yaml:

id: SampleName
pacbio:
  fasta:
    - /path/to/pacbio/file1.fasta.gz
    - /path/to/pacbio/file2.fasta.gz
    - ...
hic:
  cram:
    - /path/to/hic/hic1.cram
    - /path/to/hic/hic2.cram
    - ...
  enzymes:
    - enzyme_name_1 (e.g. DpnII)
    - enzyme_name_1 (e.g. HinfI)
    - ...

Now, you can run the pipeline using:

nextflow run sanger-tol/longreadmag \
   -profile <docker/singularity/.../institute> \
   --input input.yaml \
   --outdir <OUTDIR>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

sanger-tol/longreadmag was originally written by Jim Downie, Will Eagles, Noah Gettle.

Contributions and Support

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

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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.