Table 1.
Comprehensive list of third-party tools and algorithms used in rMAP
|
Software |
Version |
Summary |
|---|---|---|
|
Abricate |
1.0.1 |
Detection of antimicrobial resistance genes, plasmids and virulence factors |
|
AMRfinder |
3.8.4 |
Detection of antimicrobial resistance genes from assembled contigs |
|
Any2fasta |
0.4.2 |
Converts any genomic data format to fasta format |
|
Assembly-stats |
1.0.1 |
Summarizes quality assembly metrics from contigs |
|
Biopython.convert |
1.0.3 |
Conversion and manipulation of different genomic data formats |
|
BMGE |
1.12 |
Block mapping and gathering with entropy for removal of ambiguously aligned reads from multiple sequence alignments |
|
BWA |
0.7.17 |
Burrow–Wheeler algorithm for fast alignment of short sequence reads |
|
Cairosvg |
2.4.2 |
Converts SVG to PDF and PNG formats |
|
Fastqc |
0.11.9 |
Quality control and visualization of HTS data |
|
Fasttree |
2.1.10 |
Ultra-fast inference of phylogeny using the maximum-likelihood method |
|
Freebayes |
1.3.2 |
Bayesian-based haplotype prediction of nucleotide variants |
|
ISMapper |
2.0.1 |
Detection of insertion sequences within genomes |
|
IQtree |
2.0.3 |
Inference of phylogeny using the maximum-likelihood method |
|
Kleborate |
1.0.0 |
Screening for AMR genes and MLSTs from genome assemblies |
|
Lxml |
4.5.2 |
Parsing of XML and HTML using Python |
|
Mafft |
7.471 |
Algorithm for performing multiple sequence alignments |
|
Multiqc |
1.9 |
Aggregates numerous HTML quality reports into a single file |
|
Megahit |
1.2.9 |
Ultra-fast genome assembly algorithm |
|
Mlst |
2.19.0 |
Characterization and detection of clones within a population of pathogenic isolates |
|
Nextflow |
20.07.1 |
Portable next-generation workflow language that enables reproducibility and development of pipelines |
|
Parallel |
20200722 |
Executes jobs in parallel |
|
Prinseq |
0.20.4 |
Trims, filters and reformats genomic sequence data |
|
Prodigal |
2.6.3 |
Prediction of protein-coding genes in prokaryotic genomes |
|
Prokka |
1.14.6 |
Fast and efficient annotation of prokaryotic assembled genomes |
|
Quast |
5.0.2 |
Quality assembly assessment tool |
|
Roary |
3.13.0 |
Large-scale pangenome analysis |
|
R-base |
4.0.2 |
Statistical data computing and graphical software |
|
Samclip |
0.4.0 |
Filters SAM file for soft and hard clipped alignments |
|
Samtools |
1.9 |
Tools for manipulation of next-generation sequence data |
|
Shovill |
1.0.9 |
Illumina short-read assembler for bacterial genomes |
|
Snippy |
4.3.6 |
Rapid haploid bacterial variant caller |
|
Snpeff |
4.5covid19 |
Functional effect and variant predictor suite |
|
SRA-tools |
2.10.8 |
Toolbox for acquisition and manipulation of sequences from the NCBI |
|
Trimmomatic |
0.39 |
Illumina short-read adapter trimming algorithm |
|
Unicycler |
0.4.8 |
A hybrid assembly pipeline for Illumina and long-read sequence data |
|
Vt |
2015.11.10 |
A tool for normalizing variants in genomic sequence data |