Table 1.

Summary of the available bioinformatics resources for SARS-CoV-2 discovery and genomic surveillance

Databases and software	URL	Reference
Data quality control
Trimmomatic	http://www.usadellab.org/cms/index.php?page=trimmomatic	[20]
Cutadapt	https://cutadapt.readthedocs.io/en/stable/	[21]
SOAPnuke	https://github.com/BGI-flexlab/SOAPnuke	[22]
AfterQC	http://www.github.com/OpenGene/AfterQC	[23]
Fastp*	https://github.com/OpenGene/fastp	[24]
Cut_Multi_Primer.py	https://github.com/MGI-tech-bioinformatics/SARS-CoV-2_Multi-PCR_v1.0	-
NanoPack	https://github.com/wdecoster/nanopack	[45]
Porechop	https://github.com/rrwick/Porechop	-
Read mapping
Hisat2	https://daehwankimlab.github.io/hisat2/	[25]
BWA	http://bio-bwa.sourceforge.net/	[26]
Bowtie2*	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml	[27]
KMA	https://bitbucket.org/genomicepidemiology/kma	[28]
SortmeRNA	http://bioinfo.lifl.fr/RNA/sortmerna	[29]
Minimap2	https://github.com/lh3/minimap2	[46]
NGMLR	https://github.com/philres/ngmlr	[47]
MarginAlign	https://github.com/benedictpaten/marginAlign	[48]
De novo assembly
Trinity*	http://www.nature.com/nbt/index.html.	[31]
Megahit	https://hku-bal.github.io/megabox/	[32]
SPAdes	http://bioinf.spbau.ru/spades	[33]
Trans-ABySS	https://github.com/bcgsc/transabyss	[34]
PEHaplo	https://github.com/chjiao/PEHaplo	[35]
SAVAGE	https://bitbucket.org/jbaaijens/savage/src	[36]
coronaSPAdes	http://cab.spbu.ru/software/coronaspades/	[38]
Blast
Diamond*	https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/diamond/	[39]
Blastn*	ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST	[40]
Phyre2	http://www.sbg.bio.ic.ac.uk/phyre2/html	[42]
Canu	https://github.com/marbl/canu	[49]
Falcon	https://github.com/PacificBiosciences/falcon	-
Miniasm	https://github.com/lh3/miniasm	[50]
Genome visualization
IGV	http://software.broadinstitute.org/software/igv/	[43]
Geneious*	https://www.geneious.com/	-
QUAST	https://sourceforge.net/projects/quast/	[44]
SEQMAN	https://www.dnastar.com/software/molecular-biology/	-
Database
GISAID*	https://www.epicov.org/	[51]
NCBI*	https://www.ncbi.nlm.nih.gov/	[52]
CNCB/NGDC database	https://bigd.big.ac.cn/ncov/	[53]
Genome Warehouse (GWH)	https://bigd.big.ac.cn/gwh/	-
Virus Pathogen Resource (ViPR)	https://www.viprbrc.org/
Sequence alignment
CLUSTALW	https://www.genome.jp/tools-bin/clustalw	[56]
MAFFT*	https://mafft.cbrc.jp/alignment/software/	[57]
MUSCLE	http://drive5.com/muscle/	[58]
T-Coffee	http://www.tcoffee.org/	[59]
ProbCons	http://probcons.stanford.edu/	[60]
PRANK	http://wasabiapp.org/software/prank/	[62]
Bali-Phy	http://www.bali-phy.org/	[63]
StatAlign	https://dl.acm.org/doi/10.1093/bioinformatics/btn457	[64]
JABAWS	http://www.jalview.org/	[65]
EMBL-EBI	https://www.ebi.ac.uk/	[66]
webPRANK	https://www.ebi.ac.uk/goldman-srv/webprank/	[67]
Jalview	http://www.jalview.org/getdown/release/	[69]
MSAViewer	http://msa.biojs.net/index.html	[70]
AliView	http://www.ormbunkar.se/aliview/	[71]
Bioedit*	http://www.mbio.ncsu.edu/BioEdit/	[72]
Phylogenetic analysis
jMODELTEST	http://evomics.org/learning/phylogenetics/jmodeltest/	[77]
ProtTest	http://darwin.uvigo.es/software/prottest.html	[78]
TempEst	http://tree.bio.ed.ac.uk/software/tempest/	[82]
BIONJ	http://www.atgc-montpellier.fr/bionj/	[83]
PhyML	http://www.atgc-montpellier.fr/phyml/	[84]
RAxML*	http://www.exelixis-lab.org/software.html	[85]
IQ-TREE	http://www.iqtree.org/	[86]
MrBayes	http://nbisweden.github.io/MrBayes/	[87]
PhyloBayes	http://www.atgc-montpellier.fr/phylobayes/	[88]
BEAST1	http://beast.community/	[89]
BEAST2	http://www.beast2.org/	[90]
PAUP	http://paup.csit.fsu.edu/	[91]
MEGA	https://www.megasoftware.net/	[92]
PhyloSuite	http://phylosuite.jushengwu.com/	[93]
Tree visualization
Dendroscope	http://www-ab.informatik.uni-tuebingen.de/software/dendroscope	[94]
FigTree*	http://tree.bio.ed.ac.uk/software/figtree/	-
ggtree	https://yulab-smu.github.io/treedata-book/	[95]
iTOL	https://itol.embl.de/	[96]
Evolview	http://www.evolgenius.info/evolview	[97]
Genomic analysis
Pangolin COVID-19 Lineage Assigner	https://pangolin.cog-uk.io/	-
Nextstrain analysis platform*	https://nextstrain.org/	[104]
Conserved Domain Database*	https://www.ncbi.nlm.nih.gov/cdd/	[108]
UCSC	http://genome.ucsc.edu/	-
GFF2PS	http://genome.imim.es/software/gfftools/GFF2PS.html	[109]
Vectro NTI	https://www.winsite.com/vector/vector+nti/	[110]
IBS	http://ibs.biocuckoo.org/	[111]
PHYLIP	https://evolution.genetics.washington.edu/phylip.html	[112]
SimPlot*	https://sray.med.som.jhmi.edu/SCRoftware/simplot/	[114]
RDP	http://web.cbio.uct.ac.za/~darren/rdp.html	[115]
Swiss-Model program*	https://swissmodel.expasy.org/	[116]
PyMOL*	https://www.lfd.uci.edu/~gohlke/pythonlibs/	[117]

*Computer programs used by us in the discovery of SARS-CoV-2 [2, 118].