Warning
This repository has moved to https://github.com/bacterial-genomics/wf-paired-end-illumina-assembly
General schematic of the steps in the workflow
- Quick Start
- Introduction
- Installation
- Usage
- Parameters
- Resource Managers
- Output
- Troubleshooting
- Contributions and Support
- Citations
Run the built-in test set to confirm all parts are working as-expected. It will also download all dependencies to make subsequent runs much faster.
nextflow run \
wf-paired-end-illumina-assembly \
-r v1.1.0 \
-profile ,test
Example command on FastQs in "new-fastq-dir" data using SPAdes with singularity:
nextflow run \
wf-paired-end-illumina-assembly/ \
-r v1.1.0 \
-profile singularity \
--input new-fastq-dir \
--outdir my-results \
--assembler spades
Example command on FastQs in "new-fastq-dir" data using Skesa with singularity:
nextflow run \
wf-paired-end-illumina-assembly/ \
-r v1.1.0 \
-profile singularity \
--input new-fastq-dir \
--outdir my-results \
--assembler skesa
This workflow assembles bacterial isolate genomes from paired-end Illumina FastQ files. Post-assembly contig correction is performed, and a variety of quality assessment processes are recorded throughout the workflow.
This procedure can be used for all bacterial isolates (i.e., axenic, non-mixed cultures) sequenced with whole genome (WGS) or selective whole genome (SWGA) library preparation strategies. It is inappropriate for metagenomics analysis. The data files must be paired read sets (not single ended) and can come from any Illumina sequencing instrument which generates a FastQ file format (e.g., iSeq, HiSeq, MiSeq, NextSeq, NovaSeq). The read set files can be obtained from an external source, local storage device, or sequencing instrument. Other sequencing manufacturers such as Ion Torrent, PacBio, Roche 454, and Nanopore generate data files that cannot be directly used with this procedure.
- Nextflow
>=21.10.3 - Docker or Singularity
>=3.8.0 - Conda is currently unsupported
nextflow run wf-paired-end-illumina-assembly -profile <docker|singularity> --input <input directory|samplesheet> --outdir <directory for results>
Please see the usage documentation for further information on using this workflow.
Note the "--" long name arguments (e.g., --help, --input, --outdir) are generally specific to this workflow's options, whereas "-" long name options (e.g., -help, -latest, -profile) are general nextflow options.
These are the most pertinent options for this workflow:
============================================
Input/Output
============================================
--input Path to input data directory containing FastQ assemblies or samplesheet. Recognized extensions are: .fastq and .fq with optional gzip compression (.gz)
--outdir The output directory where the results will be saved.
============================================
Container platforms
============================================
-profile singularity Use Singularity images to run the workflow. Will pull and convert Docker images from Dockerhub if not locally available.
-profile docker Use Docker images to run the workflow. Will pull images from Dockerhub if not locally available.
============================================
Optional assemblers
============================================
--assembler Specify which assembler to execute (spades, skesa). [Default: spades]
============================================
Reference files
============================================
--phix_reference Path to PhiX reference file in FastA format. Recognized extensions are: {.fasta, .fas, .fa, .fna}. [Default: PhiX_NC_001422.1.fasta]
--adapters_reference Path to adapter reference file in FastA format. Recognized extensions are: {.fasta, .fas, .fa, .fna}. [Default: adapters_Nextera_NEB_TruSeq_NuGEN_ThruPLEX.fas]
PhiX reference NC_001422.1 can be obtained from NCBI.
============================================
Optional databases
============================================
--kraken1_db Path to a local directory, archive file, or a URL to compressed tar archive that contain files `database.{idx,kdb}` and `taxonomy/{names,nodes}.dmp`. [Default: MiniKraken 8GB]
--kraken2_db Path to a local directory, archive file, or a URL to compressed tar archive that contain `{hash,opts,taxo}.k2d` files. [Default: Kraken2 Standard 8GB]
--blast_db Path to a local directory, archive file, or a URL to compressed tar archive that contains BLAST 16S ribosomal RNA files. [Default: NCBI's 16S ribosomal RNA database]
--gtdb_db Path to a local directory, archive file, or a URL to compressed tar archive that contains GTDBTk database. [Default: NaN]
--busco_db Path to a local directory, archive file, or a URL to compressed tar archive that contains BUSCO lineages. Can either be a lineage dataset or entire BUSCO database. [Default: NaN]
If user does not specify inputs for parameters with a default set to NaN, these options will not be performed during workflow analysis.
View help menu of all workflow options:
nextflow run \
wf-paired-end-illumina-assembly \
-r v1.1.0 \
--help \
--show_hidden_params
The most well-tested and supported is a Univa Grid Engine (UGE) job scheduler with Singularity for dependency handling.
- UGE/SGE
- Additional tips for UGE processing are here.
- No Scheduler
- It has also been confirmed to work on desktop and laptop environments without a job scheduler using Docker with more tips here.
Please see the output documentation for a table of all outputs created by this workflow.
Q: It failed, how do I find out what went wrong?
A: View file contents in the <outdir>/pipeline_info directory.
If you would like to contribute to this pipeline, please see the contributing guidelines.
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.