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Table 1 The most commonly used tools in GalaxyTrakr based on the number of jobs run over the years 2017–2020

From: GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians

Tool ID

Use

No. of jobs run

FastQC

NGS Quality assessment

39750

SNP_pipeline a

SNP identification

36685

Trimmomatic

NGS Quality assessment

25138

SkesaMLST

Short-read assembly and MLST Typing

17641

SPAdes

Short-read assembly

13962

SeqSero

Salmonella Serotyping

10788

Fastq_dump_paired

Paired Fastq reads download

9514

ABRicate

Antimicrobial Resistance

8520

AMRFinder

Antimicrobial Resistance

6976

SKESA

Short-read assembly

5791

Ectyper

E. coli serotyping

5237

QUAST

Quality assessment

4475

Kraken2

Metagenomics classification

4433

shovill

Short-read assembly

3760

MetaPhlan2

Metagenomics classification

2685

RAxML

Phylogenetics

2649

Mlst

MLST Typing

1711

Prokka

Genome annotations

1382

Confindr

Bacterial contamination detection

1110

Btyper

Classification of Bacillus cereus group

1077

SRST2

Short-read sequence typing

1050

Mitokmer a

Metagenomics eukaryotic prediction

975

Sistr_cmd

in silico serotyping

933

Metaspades

Metagenomics assembly

725

Newick Display

Phylogenetics display

720

Bwa_mem

Short-read mapping

637

  1. aTools that are specifically designed for GalaxyTrakr users