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

• braken: https://ccb.jhu.edu/software/bracken/

• metaphlan3: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-3.0

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/

• CircularMapper: https://github.com/apeltzer/CircularMapper/blob/master/docs/contents/userguide.rst

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