tadrep 0.9.2

Description:

tadrep 0.9.2

TaDReP: Targeted Detection and Reconstruction of Plasmids
TaDReP is a tool for the rapid targeted detection and reconstruction of plasmids within bacterial draft genomes.

Description
Installation
Input & Output
Overview
Usage

Setup
Database
Extract
Characterize
Cluster
Detect
Visualize


Issues & Feature Requests

Description
TaDReP facilitates the rapid screening for target plasmids within single or cohorts of draft genomes.
It detects and reconstructs reference plasmids within bacterial draft assemblies via Blast+ alignments of draft genome contigs that are rigourously filtered for coverage and sequence identity thresholds. Finally, reference plasmids are detected and reconstructed if strict thresholds regarding plasmid-wise coverage and sequence identity are met.
Installation
TaDRep can be installed via Conda and Pip. However, we encourage to use Conda to automatically install all required 3rd party dependencies.
Conda
conda install -c conda-forge -c bioconda tadrep

Pip
$ python3 -m pip install --user tadrep

Input and Output
Input
TaDReP accepts bacterial draft genome assemblies in (zipped) fasta format. Complete reference plasmid sequences are either extracted from (semi-)closed genomes or plasmid sequence collections, or created from public plasmid databases (RefSeq / PLSDB). For further information how to extract plasmid sequences, please read the extract section below.
Output
For each draft genome TaDReP writes a TSV summary file providing all detected reference plasmids and aligned genome contigs. For each reference plasmid that was detected in a draft assembly, ordered and rearranged contigs are exported as N-merged scaffolds, as well as mere contigs. Furthermore, for each reconstructed plasmid, the reference plasmid backbone and all contig alignments are visualized (PDF).

<genome>-summary.tsv: detailed per contig alignment summary
<genome>-<plasmid>-contigs.fna: ordered and rearranged contigs of the reconstructed plasmid
<genome>-<plasmid>-pseudo.fna: pseudomolecule sequence of the reconstructed plasmid
<genome>-<plasmid>.pdf: visualization of aligned contigs against the detected reference plasmid

If multiple genomes are provided, TaDReP also provides a presence/absence matrix of all detected plasmids as a cohort analyses, as well as a short summary of plasmids and which contigs were matched in each genome.

plasmids.info: plasmid characterization summary
plasmids.tsv: presence/absence table of detected plasmids
summary.tsv: short summary of matched contigs through all genomes
tadrep.log: log-file for debugging

Overview

Usage
TaDReP's workflow comprises seven steps implement in CLI submodules to ease semi-automated multi-step analyses.
usage: TaDReP [--help] [--verbose] [--threads THREADS] [--tmp-dir TMP_DIR] [--version] [--output OUTPUT] [--prefix PREFIX] ...

Targeted Detection and Reconstruction of Plasmids

General:
--help, -h Show this help message and exit
--verbose, -v Print verbose information
--threads THREADS, -t THREADS
Number of threads to use (default = number of available CPUs)
--tmp-dir TMP_DIR Temporary directory to store blast hits
--version show program's version number and exit

General Input / Output:
--output OUTPUT, -o OUTPUT
Output directory (default = current working directory)
--prefix PREFIX Prefix for all output files (default = None)

Submodules:

setup Download and prepare inc-types
database Download and create database for TaDReP
extract Extract unique plasmid sequences
characterize Identify plasmids with GC content, Inc types, conjugation genes
cluster Cluster related plasmids
detect Detect and reconstruct plasmids in draft genomes
visualize Visualize plasmid coverage of contigs

Citation:
Schwengers et al. (2023)
TaDReP: Targeted Detection and Reconstruction of Plasmids.
GitHub https://github.com/oschwengers/tadrep

Setup
The setup module downloads external databases, e.g. PlasmidFinders incompatibility groups that are required to characterize plasmids.
Example
Verbosely download inc-types:
tadrep -v -o <output-path> setup

Database
The database module downloads public plasmid databases (PLSDB / RefSeq) into a reference plasmid file. This creates a subdirectory in a user specified output directory.
If you downloaded a database, you can skip the extract step and start with the characterization.
usage: TaDReP database [-h] [--type {refseq,plsdb}] [--force]

options:
-h, --help show this help message and exit

Input / Output:
--type {refseq,plsdb}
External DB to import (default = 'refseq')
--force, -f Force download and new setup of database

Examples
Create refseq database:
tadrep -v -o <output-path> database --type refseq

Create PLSDB database:
tadrep -v -o <output-path> database --type plsdb

Overwrite existing refseq files with newly downloaded data.
tadrep -v -o <output-path> database --type refseq -f

Extract
The extract module Extracts reference plasmid sequences from complete genomes, (semi-)draft genomes or plasmid files.
usage: TaDReP extract [-h] [--type {genome,plasmid,draft}] [--header HEADER] [--files FILES [FILES ...]] [--discard-longest DISCARD_LONGEST] [--max-length MAX_LENGTH]

options:
-h, --help show this help message and exit

Input:
--type {genome,plasmid,draft}, -t {genome,plasmid,draft}
Type of input files
--header HEADER Template for header description inside input files: e.g.: header: ">pl1234" --> --header "pl"
--files FILES [FILES ...], -f FILES [FILES ...]
File path
--discard-longest DISCARD_LONGEST, -d DISCARD_LONGEST
Discard n longest sequences in output
--max-length MAX_LENGTH, -m MAX_LENGTH
Max sequence length (default = 1000000 bp)

For different input types specified via --type:

genome: extract all but the longest sequence. This can be adjusted via --discard-longest.
draft: extracts only sequences with specific headers. Headers can be specified via --header.
plasmid: extracts all sequences from a given file without any filtering.

If you extracted references, you can skip the database step and start with the characterization.
Examples
Extract all sequences from file plasmids.fna ignoring the two longest:
tadrep -v --type genome --discard-longest 2 --files plasmids.fna

Extract all sequences from file plasmids.fna where header contains pl:
tadrep -v --type draft --header "pl" --files plasmids.fna

Extract all potential plasmid sequences (one of 'plasmid', 'complete', 'circular=true' in header) from file plasmids.fna ignoring sequences longer than 500000 bp:
tadrep -v --type draft --max-length 500000 --files plasmids.fna

Extract all sequences from file plasmids.fna:
tadrep -v --type plasmid --files plasmids.fna

Characterize
The characterize module characterizes all reference plasmids by the following features:

Length
GC content
Incompatibility types
Number of coding sequences

If you downloaded a reference database this is the step to start with.
usage: TaDReP characterize [-h] [--db DATABASE] [--inc-types INC_TYPES]

optional arguments:
-h, --help show this help message and exit

Input:
--db DATABASE Import json file from a given database path into working directory
--inc-types INC_TYPES
Import inc-types from given path into working directory

Examples
Characterize plasmids in working directory <output-path> and import inc-types from inc-types folder:
tadrep -v -o <output-path> characterize --inc-types inc-types/inc-types.fasta

If inc-types is already present inside the working directory, the parameter --inc-types can be omitted:
tadrep -v -o <output-path> characterize

If you downloaded a database you can import it into the working directory <output-path> with the --db parameter:
tadrep -v -o <output-path> characterize --db databases/plsdb/plsdb.json --inc-types inc-types/inc-types.fasta

Cluster
The cluster module groups plasmids with similar sequences and features.
usage: TaDReP cluster [-h] [--min-sequence-identity [1-100]] [--max-sequence-length-difference [1-1000000]] [--skip]

options:
-h, --help show this help message and exit

Parameter:
--min-sequence-identity [1-100]
Minimal plasmid sequence identity (default = 90%)
--max-sequence-length-difference [1-1000000]
Maximal plasmid sequence length difference in basepairs (default = 1000)
--skip, -s Skips clustering, one group for each plasmid

Example
tadrep -v cluster

Detect
The detect module aligns contigs of bacterial draft genomes to reference plasmids using BLAST+. Each match is evaluated by coverage and sequence identity of the aligned plasmid section and can be individualy adjusted by using --min-plasmid-identity and --min-plasmid-coverage. If various contigs match a plasmid and the combined coverage and identity exceed a certain threshold, the combination of aligned contigs is saved.
Each detected plasmid is reconstructed as a pseudo sequence, where matching contigs are linked by a sequence of N. Information on detected & reconstructed plasmids and in which draft genomes they were found in provided in a summary and a presence-absence table.
usage: TaDReP detect [-h] [--genome GENOME [GENOME ...]] [--min-contig-coverage [1-100]] [--min-contig-identity [1-100]] [--min-plasmid-coverage [1-100]] [--min-plasmid-identity [1-100]]
[--gap-sequence-length GAP_SEQUENCE_LENGTH]

optional arguments:
-h, --help show this help message and exit

Input / Output:
--genome GENOME [GENOME ...], -g GENOME [GENOME ...]
Draft genome path

Annotation:
--min-contig-coverage [1-100]
Minimal contig coverage (default = 90%)
--min-contig-identity [1-100]
Maximal contig identity (default = 90%)
--min-plasmid-coverage [1-100]
Minimal plasmid coverage (default = 80%)
--min-plasmid-identity [1-100]
Minimal plasmid identity (default = 90%)
--gap-sequence-length GAP_SEQUENCE_LENGTH
Gap sequence N length (default = 10)

Examples
Detect reference plasmids from directory <output-path> in file draft.fna with default settings:
tadrep -v -o <output-path> detect --genome draft.fna

Detect reference plasmids from directory <output-path> in file draft.fna;
75% of contig length has to be covered by a match;
Combined contig matches have to cover at least 95% of reference plasmid length:
tadrep -v -o <output-path> detect --genome draft.fna --min-contig-coverage 75 --min-plasmid-coverage 95

Detect reference plasmids from directory <output-path> in file draft.fna;
Contig sequence of a match has to be at least 80% identical to reference plasmid;
Combined contig matches have to sum up to at least 95% identity of reference plasmid sequence:
tadrep -v -o <output-path> detect --genome draft.fna --min-contig-identity 80 --min-plasmid-identity 95

Note: --min-contig-coverage / --min-plasmid-identity and --min-contig-identity / --min-plasmid-coverage can be combined as well.
Visualize
The visualize module visualizes matching contigs from draft genomes for each detected plasmid.
By default, contigs are represented by boxes, either on top or bottom of the plasmid center line. The position of the boxes represents a match on either forward or backward strand respectively. A colour gradient is used to indicate the identity between contig and plasmid section, a brighter colorization implies smaller sequence identity. The start of this gradient, where it is the brightest, can be individually set with the --interval-start parameter.
usage: TaDReP visualize [-h] [--plotstyle {bigarrow,arrow,bigbox,box,bigrbox,rbox}] [--labelcolor LABELCOLOR] [--linewidth LINEWIDTH] [--arrow-shaft-ratio ARROW_SHAFT_RATIO] [--size-ratio SIZE_RATIO]
[--labelsize LABELSIZE] [--labelrotation LABELROTATION] [--labelhpos {left,center,right}] [--labelha {left,center,right}] [--interval-start [0-100]] [--number-of-intervals [1-100]]
[--omit_ratio [0-100]]

optional arguments:
-h, --help show this help message and exit

Style:
--plotstyle {bigarrow,arrow,bigbox,box,bigrbox,rbox}
Contig representation in plot
--labelcolor LABELCOLOR
Contig label color
--linewidth LINEWIDTH
Contig edge linewidth
--arrow-shaft-ratio ARROW_SHAFT_RATIO
Size ratio between arrow head and shaft
--size-ratio SIZE_RATIO
Contig size ratio to track

Label:
--labelsize LABELSIZE
Contig label size
--labelrotation LABELROTATION
Contig label rotation
--labelhpos {left,center,right}
Contig label horizontal position
--labelha {left,center,right}
Contig label horizontal alignment

Gradient:
--interval-start [0-100]
Percentage where gradient should stop
--number-of-intervals [1-100]
Number of gradient intervals

Omit:
--omit_ratio [0-100] Omit contigs shorter than X percent of plasmid length from plot

Examples
Visualize results from detection in directory <output-path> with default settings:
tadrep -v -o <output-path> visualize

Visualize results from detection in directory sho<output-path>wcase;
Brightest colour of gradient starts at 95.5% sequence identity (darkest colour is always 100% identity);
Surround contig blocks with 1px line:
tadrep -v -o <output-path> visualize --interval-start 95.5 --linewidth 1

Issues & Feature Requests
TaDReP is brand new and like in every software, expect some bugs lurking around. So, if you run into any issues with TaDReP, we'd be happy to hear about it.
Therefore, please, execute it in verbose mode (-v) and do not hesitate to file an issue including as much information as possible:

a detailed description of the issue
command line output
log file (tadrep.log)
a reproducible example of the issue with an input file that you can share if possible