| parallel-fastq-dump |
0.6 |
Parallel wrapper for SRA Toolkit |
https://github.com/rvalieris/parallel-fastq-dump |
prefetch <sra_id> && parallel-fastq-dump --sra-id <sra_id> --threads 1 --split-3 |
| Trimmomatic |
0.38 |
Trimming tool for Illumina NGS reads |
https://github.com/timflutre/trimmomatic |
trimmomatic PE -threads 1 <input_read_pair_1.fq> <input_read_pair_2.fq> <input_read_pair_1_trimmed.fastq> <input_read_unpair_1_trimmed.fastq> <input_read_pair_2_trimmed.fastq> <input_read_unpair_2_trimmed.fastq> HEADCROP:15 CROP:200 LEADING:10 TRAILING:10 SLIDINGWINDOW:5:20 MINLEN:50 |
| FastQC |
0.11 |
Tool to quality control for sequencing data |
https://github.com/s-andrews/FastQC |
fastqc <input_read_pair_1_trimmed.fastq> <input_read_pair_2_trimmed.fastq> --extract |
| SPAdes |
3.13 |
Genome assembler |
https://github.com/ablab/spades |
spades.py -t 1 -1 <input_read_pair_1_trimmed.fastq> -2 <input_read_pair_2_trimmed.fastq> --careful --cov-cutoff auto -o <spades_output> --phred-offset 33 |
| QUAST |
5.0 |
Evaluation tool for genome assembly |
https://github.com/ablab/quast |
quast --fast -o <quast_output> <spades_output/contigs.fasta> |
| PlasmidFinder |
2.0 |
Tool for detection and characterization of plasmid sequences |
https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ |
plasmidfinder.py -p $PLASMID_DB -i <spades_output/contigs.fasta> -o <plasmidfinder_output> |
| SISTR |
1.0 |
Tool for Salmonella In Silico Typing |
https://github.com/phac-nml/sistr_cmd |
sistr --qc -vv --alleles-output <allele_results.json> --novel-alleles <novel_alleles.fasta> --cgmlst-profiles <cgmlst_profiles.csv> -f csv -o <sistr_output.csv> <spades_output/contigs.fasta> |
| Prokka |
1.13 |
Prokaryotic genome annotation tool |
https://github.com/tseemann/prokka |
prokka --kingdom Bacteria --locustag <sra_id> --outdir <prokka_output> --prefix <sra_id> --force <spades_output/contigs.fasta> |
| Roary |
3.12 |
Pan-genome and core-genome alignment tool |
https://github.com/sanger-pathogens/Roary |
roary -s -e --mafft -p 4 -cd 99.0 -i 95 -f <prokka_output/sra_id.gff> |
| fastbaps |
1.0 |
Improved version of the BAPS clustering method |
https://github.com/gtonkinhill/fastbaps |
Rscript fastbaps.R <roary_output/core_gene_alignment.aln> <fastbaps_output.csv> |
| MLST |
2.16 |
Tool for multilocus-sequence typing |
https://github.com/tseemann/mlst |
mlst --legacy --scheme senterica --csv <spades_output/contigs.fasta> |
| ABRicate |
1.0 |
Tool for screening of contigs for AMR and virulence genes |
https://github.com/tseemann/abricate |
abricate --db <abricate_db> --csv <spades_output/contigs.fasta> |