NTMscope-MAC

This repository comprizes essential scripts and code that have been used in the bioinformatical analyses of the whole genome sequencing project NTMscope-MAC. Single bioinformatic tools are summarized below. Sequencing data can be accessed in the European Nucleotide Archive under project number PRJEB70863.

An additional interactive visualisation of our dataset can be accessed via https://microreact.org/project/ntmscope-mac.

Further information on NTMscope-related projects can be found on https://www.ntmscope.org.

Used bioinformatic tools and scripts

Dependencies of the used bioinformatical tools are not shown.

NTMseq pipeline

• Most of the scripts below have been implemented in the NTMseq pipeline (Most recent version on https://github.com/ngs-fzb/NTMtools/tree/main/scripts/NTMseq)

Quality control

• Fastqc v. 0.11.9 (https://github.com/s-andrews/FastQC)
• fastqc_all.sh (custom script)
• Multiqc v. 1.13 (https://multiqc.info/)

Removal of adapter sequences

• Fastp v. 0.23.2 (https://github.com/OpenGene/fastp)
• starter_fastp_DefaultSettings.sh

Simulation of reads for assembled sequence data

• dwgsim v. 0.1.12-13 (https://github.com/nh13/DWGSIM)
• starter_dwgsim_artificial_fastq.v01_MD3.sh

Species designation

• NTM-Profiler v. 0.2.0 (https://github.com/jodyphelan/NTM-Profiler)
• ntm_profiler_all.sh (custom script)
• ntm_profiler_extractor.R (custom script)
• Type Strain Genome Server, TYGS (https://tygs.dsmz.de/)
• fastANI (https://github.com/ParBLiSS/FastANI)

Phylogeny

• MTBseq v. 1.1.0 (https://github.com/ngs-fzb/MTBseq_source)

MTBseq --step TBfull --ref M._avium_DSM44156 --threads YOUR_THREADS --continue --sample YOUR_SAMPLE_LIST

• exploratory_tree_upgma.R (custom script)
• Raxml v. 8.2.12 (https://github.com/stamatak/standard-RAxML)

raxmlHPC -f a -m GTRGAMMA -s XX_amended_u95_phylo.fasta -n YOUR_NAME -x 12345 -p 12345 -# 500

• shovill v. 1.1.0 (https://github.com/tseemann/shovill)
• shovil_all.sh (custom script)
• Mashtree v.1.2.0
• starter_Mashtree.sh
• transmission_cluster_identifier.R (custom script)
• Microreact (https://microreact.org/)
• Microreact project (https://microreact.org/project/wUatE2dwuoHnCH7G4petvb-ntmscope-mac)

Genome annotation

• Prokka v. 1.14.6. (https://github.com/tseemann/prokka)
• prokka_all.sh (custom script)

Plasmid analysis

• SRST2 v.0.2.0 (https://katholt.github.io/srst2/) using a custom database of 152 NTM plasmids downloaded from PLSDB v.2021-06-23-v2
• starter_customDB_SRST2.sh and customDB_to_SRST2.db
• Roary v.3.13.0 (https://github.com/sanger-pathogens/Roary/blob/master/README.md)

Resistance prediction

• AMRfinderPlus v.3.11.2
• ariba v. 2.14.4 (https://github.com/sanger-pathogens/ariba)
• Mab_ariba (https://github.com/samlipworth/Mab_ariba)
• MAC_ariba_analyser.R (custom script)

Network analysis

• patient_combinations.R (custom script)
• transmission_forloop.R (custom script)