1. List of Tools

Data preprocessing

• AdapterRemoval: https://github.com/MikkelSchubert/adapterremoval

Metagenomics screening of shotgun data

• kraken: https://ccb.jhu.edu/software/kraken/
• kraken2: https://ccb.jhu.edu/software/kraken2/index.shtml
• krona: https://github.com/marbl/Krona/wiki

Reads alignment and variants calling

• bwa: https://github.com/lh3/bwa
• gatk: https://software.broadinstitute.org/gatk/
• samtools: http://www.htslib.org/
• bcftools: http://www.htslib.org/

Filtering and manipulating bam files

• picard: https://broadinstitute.github.io/picard/
• dedup: https://github.com/apeltzer/DeDup

aDNA deamination detection and rescalinghttps://github.com/Amine-Namouchi/snpToolkit

• mapDamage: https://ginolhac.github.io/mapDamage/

Creating summary reports

• fastqc: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
• Qualimap: http://qualimap.bioinfo.cipf.es/
• BAMStats: http://bamstats.sourceforge.net
• MultiQC: http://multiqc.info/

Integrative genomic viewer

• IGV: http://software.broadinstitute.org/software/igv/

SNPs annotation and post-processing

• snpToolkit: https://github.com/Amine-Namouchi/snpToolkit

Phylogeny

• IQ-TREE: http://www.iqtree.org/
• Figtree: http://tree.bio.ed.ac.uk/software/figtree