Plastaumatic: An automated pipeline to assemble and annotate plastome sequences
Introduction
plastaumatic
is an automated pipeline developed for both assembly and annotation of plastomes, with the scope of the researcher being able to load whole genome sequence data with minimal manual input, and therefore a faster runtime. The main structure of the current automated pipeline includes trimming of adaptor and low-quality sequences using fastp
, de novo plastome assembly using NOVOPlasty
, standardization and quality checking of the assembled genomes through a custom script utilizing BLAST+
and SAMtools
, annotation of the assembled genomes using AnnoPlast
, and finally generating required files for NCBI GenBank submissions.
This repository includes a snakefile
which uses Snakemake
workflow manager to perform all the tasks. Also, a shell executable that does the same.
Pre-requisites:
Snakemake v5.10.0+
[if using the Snakemake
pipeline]
fastp v0.23.0
NOVOPlasty v4.3.1
Python v3.8
BioPython v1.79
& pandas v1.4.3
(for AnnoPlast
)
Blast+ v2.12.0
samtools v1.9
installation
Simply clone this repository in your desired destination and add to your PATH
git clone https://github.com/stromviklab/plastaumatic.git
export PATH=$(pwd)/plastaumatic:$PATH
echo 'export PATH='$(pwd)'/plastaumatic:$PATH' >> ~/.bashrc
how-to-run (Snakemake)
-
Before running the Snakemake pipeline, make sure all the pre-requisites are installed and available in your PATH
-
Make sure to edit the
config.yaml
file before your run (a templateconfig.yaml
file is available from the repository)
seed: Test_dataset/seed.fasta # path to a seed fasta file for NOVOPlasty (see: https://github.com/ndierckx/NOVOPlasty)
ref_gb: Test_dataset/reference.gb # path to a reference GenBank file for annotation (see: https://github.com/SaiReddy-A/AnnoPlast)
range: 140000-160000 # estimated plastome size range
repo: plastaumatic # path to the plastaumatic repository
novo_path: /mnt2/software/NOVOPlasty/NOVOPlasty4.3.1.pl # path to the NOVOPlasty executable
samples: # prefix and reads of one/many genomes go under samples
genome1: Test_dataset/test1.fq.gz,Test_dataset/test2.fq.gz # prefix: forward_read,revese_read
- If you want to run this pipeline on multiple genomes, just add more lines below
samples
in this format:
samples:
genome1: forward.fq,reverse.fq
genome2: forward.fq,reverse.fq
genome3: forward.fq,reverse.fq
...
...
genomeX: forward.fq,reverse.fq
- Copy the
snakefile
to your preferred output directory. Modify the path to config file in thesnakefile
and run
snakemake
how-to-run (shell script)
- Before running the
plastaumatic
executable, make sure all the pre-requisites are installed and available in your PATH - run
plastaumatic -h
for help
Usage: plastaumatic -s seed.fa -g reference.gb -r <140000-160000> -f fof.txt -n NOVOPlasty4.3.1.pl
options:
-s Path to the seed file for assembly</br>
-g Path to the reference GenBank file</br>
-r Plastome assembly size range [140000-160000]</br>
-f Path to the file-of-filenames with reads</br>
-n Path to NOVOPlasty executable</br>
-h Shows this help message</br>
- The file-of-filenames is a simple txt file with comma seperated prefix and read files of one/many genomes
genome1,forward.fq,reverse.fq
genome2,forward.fq,reverse.fq
genome3,forward.fq,reverse.fq
- An example
plastaumatic
run
plastaumatic -s Test_dataset/seed.fasta -g Test_dataset/reference.gb -r 140000-160000 -f readList.txt -n software/NOVOPlasty/NOVOPlasty4.3.1.pl
$ cat readList.txt
genome1,Test_dataset/test1.fq.gz,Test_dataset/test2.fq.gz
Output files
For each genome a prefix directory is created from where the pipeline is run. Each prefix directory contains
prefix
├── 00-logs
├── 01-trim
├── 02-assemble
├── 03-standardize
├── 04-annotate
├── 05-tbl
├── prefix_config.txt
├── prefix.plastome.fa # a symlink to the final plastome assembly file
└── prefix.plastome.gb # a symlink to the final plastome annotation file
Citations
Chen W, Achakkagari SR and Strömvik M (2022) Plastaumatic: Automating plastome assembly and annotation. Front. Plant Sci. 13:1011948. doi: 10.3389/fpls.2022.1011948
Since plastaumatic
uses multiple software in its pipeline, publishing the results obtained form plastaumtic
should also cite the following sources
- Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i884–i890, https://doi.org/10.1093/bioinformatics/bty560
- Dierckxsens, N., Mardulyn, P., & Smits, G. (2017). NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic acids research, 45(4), e18. https://doi.org/10.1093/nar/gkw955
- Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009 Dec 15;10:421. doi: 10.1186/1471-2105-10-421. PMID: 20003500; PMCID: PMC2803857
- Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352