Table S1: Giant Virus Finder Workflow on the Command Level

Supplementary information for the article: “The Giant Virus Finder Discovers an Abundance of Giant Viruses in the Antarctic Dry Valleys” by Csaba Kerepesi & Vince Grolmusz

Figure S1: The number of giant virus reads found is visualized in each metagenome deposited at http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeProject&project=2997. This figure is the metagenome-filename labelled version of Figure 1 in the main text.

TABLE S1: GIANT VIRUS FINDER WORKFLOW ON THE COMMAND LEVEL:

- Prerequisites: Perl 5.14.2 or later, Python 2.7, Biopython 1.5 or later

- Start from the ~/GiantVirusFinder directory

- Download all Giant Virus Finder files to GiantVirusFinder directory

***Making Giant Virus Toplist:

- mkdir AllVirusGenome

- wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Viruses/all.fna.tar.gz

- tar xvzf

- cd ..

- mkdir TopGiants-gb-300k

- cd TopGiants-gb-300k

- python ../TopGiantsEntrez.py 1

- cd ..

- perl TopGiants.pl TopGiants-gb-300k/TopGiants-gb-300k.csv 300000

***Installing Stand alone UNIX BLAST:

- cd ~

- wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.2.30+-x64-linux.tar.gz

- tar xvzf

- mkdir ncbi-blast-2.2.30+/db

- cd ncbi-blast-2.2.30+/db

- wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt*

- ls *.gz | while read line; do tar xvzf $line; done

- cd ~/GiantVirusFinder

***Building metagenome database:

- mkdir 16SoilMetagenome

- cd 16SoilMetagenome

- Download the 16 soil metagenomes: http://metagenomics.anl.gov/metagenomics.cgi?page=MetagenomeProject&project=2997

- Convert the fastq files to fasta

- ls *.fasta > ../mgm.list

- ls *.fasta | while read line; do ~/ncbi-blast-2.2.30+/bin/makeblastdb -dbtype nucl -in $line -out ~/ncbi-blast-2.2.30+/db/$line; done

- cd ..

***Giant Virus Finding, Phase1:

- mkdir Giants-in-16Soil-metagenomes

- perl Phase1Blast-MultiCore.pl Giants-in-16Soil-metagenomes > Giants-in-16Soil-metagenomes/log-Phase1Blast-MultiCore.pl.txt

- perl Concat.pl Giants-in-16Soil-metagenomes

- perl GetCandidateReads.pl Giants-in-16Soil-metagenomes 16SoilMetagenome

***Giant Virus Finding, Phase2:

- perl Phase2Blast-MultiCore.pl Giants-in-16Soil-metagenomes > Giants-in-16Soil-metagenomes/log-Phase2Blast-MultiCore.pl.txt

- perl GiantVirusFinder-Multi.pl Giants-in-16Soil-metagenomes 0.2

- perl CountGiants.pl Giants-in-16Soil-metagenomes 0.2

- perl blastx-Multi.pl Giants-in-16Soil-metagenomes 0.2

Table S2: The list of virus sequences with larger than 300 kbp length. Reference genome data are taken from the ftp://ftp.ncbi.nlm.nih.gov/genomes/Viruses/all.fna.tar.gz file from the NCBI Genome FTP. Note that the length of distinct genome sequences (segments) belonged to a single genome are summed. Further sequences are added from the NCBI Nucleotide database using the search term: "Viruses"[Organism] AND 300000:10000000[Sequence Length] NOT "Bacteria"[Organism] NOT "Archaea"[Organism].

Those partial or complete genomes of the same species that are referred to with different accession numbers, are listed separately with their respective database accession numbers (e.g., Emiliania huxleyi virus 86 sequences are present in lines 29 and 30; Lausannevirus and Lausannevirus isolate 7715, both with complete genomes, are present in lines 55 and 56, respectively.)

Sequence title / Length / Segm. / Accession
1 / Pandoravirus salinus, complete genome / 2473870 / 1 / NC_022098.1
2 / Pandoravirus inopinatum isolate KlaHel, complete genome / 2243109 / 1 / NC_026440.1
3 / Pandoravirus dulcis, complete genome / 1908524 / 1 / NC_021858.1
4 / Megavirus chiliensis, complete genome / 1259197 / 1 / NC_016072.1
5 / Megavirus courdo11, complete genome / 1246126 / 1 / JX975216.1
6 / Megavirus terra1 genome / 1244621 / 1 / NC_023640.1
7 / Megavirus lba isolate LBA111, complete genome / 1230522 / 1 / NC_020232.1
8 / Samba virus, partial genome / 1212735 / 1 / KF959826.1
9 / Acanthamoeba castellanii mamavirus strain Hal-V, complete genome / 1191693 / 1 / JF801956.1
10 / Acanthamoeba polyphaga mimivirus, complete genome / 1181549 / 1 / NC_014649.1
11 / Hirudovirus strain Sangsue, complete genome / 1181042 / 1 / KF493731.1
12 / Mimivirus terra2 genome / 1168989 / 1 / NC_023639.1
13 / Acanthamoeba polyphaga moumouvirus, complete genome / 1021348 / 1 / NC_020104.1
14 / UNVERIFIED: Moumouvirus goulette, complete genome / 1016844 / 1 / KC008572.1
15 / Acanthamoeba polyphaga mimivirus isolate M4, complete genome / 981813 / 1 / JN036606.1
16 / Acanthamoeba polyphaga lentillevirus contig00005, whole genome shotgun sequence / 788571 / 1 / AFYC01000005.1
17 / Cafeteria roenbergensis virus BV-PW1, complete genome / 617453 / 1 / NC_014637.1
18 / Pithovirus sibericum isolate P1084-T, complete genome / 610033 / 1 / NC_023423.1
19 / Cotesia congregata virus complete genome, segment Circle21 / 567670 / 30 / NC_006652.1
20 / Megavirus courdo7 isolate Mv13-c7, partial genome / 529672 / 1 / JN885991.1
21 / Cotesia congregata bracovirus proviral locus 2 (PL2) / 522749 / 1 / HF586473.1
22 / Bacillus phage G, complete genome / 497513 / 1 / NC_023719.1
23 / Phaeocystis globosa virus 12T, *** SEQUENCING IN PROGRESS ***, 3 unordered pieces / 460002 / 1 / HQ634147.1
24 / Phaeocystis globosa virus strain 16T, complete genome / 459984 / 1 / NC_021312.1
25 / Phaeocystis globosa virus 14T, *** SEQUENCING IN PROGRESS ***, 3 unordered pieces / 452892 / 1 / HQ634144.1
26 / Emiliania huxleyi virus 207, *** SEQUENCING IN PROGRESS ***, 16 unordered pieces / 421891 / 1 / JF974317.1
27 / Emiliania huxleyi virus 208, *** SEQUENCING IN PROGRESS ***, 17 unordered pieces / 411003 / 1 / JF974318.1
28 / Emiliania huxleyi virus 202, *** SEQUENCING IN PROGRESS ***, 12 unordered pieces / 407516 / 1 / HQ634145.1
29 / Emiliania huxleyi virus 86 isolate EhV86 / 407339 / 1 / AJ890364.1
30 / Emiliania huxleyi virus 86, complete genome / 407339 / 1 / NC_007346.1
31 / Emiliania huxleyi virus 201, *** SEQUENCING IN PROGRESS ***, 7 unordered pieces / 407301 / 1 / JF974311.1
32 / Emiliania huxleyi virus 164 partial genome sequence / 401558 / 1 / KF481688.1
33 / Emiliania huxleyi virus 18 partial genome sequence / 400762 / 1 / KF481685.1
34 / Emiliania huxleyi virus 203, *** SEQUENCING IN PROGRESS ***, 7 unordered pieces / 400520 / 1 / JF974291.1
35 / Emiliania huxleyi virus 156 partial genome sequence / 400341 / 1 / KF481687.1
36 / Emiliania huxleyi virus 145 partial genome sequence / 399873 / 1 / KF481686.1
37 / Emiliania huxleyi virus 88, *** SEQUENCING IN PROGRESS ***, 8 unordered pieces / 397298 / 1 / JF974310.1
38 / Emiliania huxleyi virus 84, *** SEQUENCING IN PROGRESS ***, 9 unordered pieces / 396620 / 1 / JF974290.1
39 / Insectomime virus strain V478, partial genome / 386631 / 1 / KF527888.1
40 / Insectomime virus V478 genomic scaffold, scaffold00001, whole genome shotgun sequence / 382785 / 1 / HG428764.1
41 / Tunisvirus fontaine2 strain U484, complete genome / 380011 / 1 / KF483846.1
42 / Emiliania huxleyi virus 99B1 draft genome sequence / 376759 / 1 / FN429076.1
43 / Cannes 8 virus, complete genome / 374041 / 1 / KF261120.1
44 / Aureococcus anophagefferens virus isolate BtV-01, complete genome / 370920 / 1 / NC_024697.1
45 / Melbournevirus isolate 1, complete genome / 369360 / 1 / NC_025412.1
46 / Paramecium bursaria Chlorella virus NY2A Chlorella virus NY2A ctg_13 genomic sequence / 368683 / 1 / DQ491002.1
47 / Paramecium bursaria Chlorella virus NY2A, complete genome / 368683 / 1 / NC_009898.1
48 / Marseillevirus marseillevirus strain T19, complete genome / 368454 / 1 / NC_013756.1
49 / Canarypox virus strain ATCC VR-111, complete genome / 359853 / 1 / AY318871.1
50 / Canarypox virus, complete genome / 359853 / 1 / NC_005309.1
51 / Cronobacter phage vB_CsaM_GAP32, complete genome / 358663 / 1 / NC_019401.1
52 / Escherichia phage 121Q, complete genome / 348532 / 1 / NC_025447.1
53 / Paramecium bursaria Chlorella virus NYs1, partial genome / 348463 / 1 / JX997183.1
54 / Escherichia phage PBECO 4, complete genome / 348113 / 1 / KC295538.1
55 / Lausannevirus, complete genome / 346754 / 1 / NC_015326.1
56 / Lausannevirus isolate 7715, complete genome / 346754 / 1 / HQ113105.1
57 / Klebsiella phage K64-1 DNA, complete genome / 346602 / 1 / AB897757.1
58 / Enterobacteria phage vB_KleM-RaK2, complete genome / 345809 / 1 / NC_019526.1
59 / Moumouvirus Monve isolate Mv13-mv, partial genome / 345413 / 1 / JN885998.1
60 / Paramecium bursaria Chlorella virus IL-5-2s1, partial genome / 345255 / 1 / JX997170.1
61 / Paramecium bursaria Chlorella virus NY-2B, partial genome / 344863 / 1 / JX997182.1
62 / Organic Lake phycodnavirus 1 genomic sequence / 344723 / 1 / HQ704802.1
63 / Paramecium bursaria Chlorella virus AR158, complete genome / 344691 / 1 / NC_009899.1
64 / Paramecium bursaria Chlorella virus AR158 genomic sequence / 344691 / 1 / DQ491003.2
65 / Paramecium bursaria Chlorella virus MA-1D, partial genome / 339653 / 1 / JX997172.1
66 / Paramecium bursaria Chlorella virus MA-1E, partial genome / 339391 / 1 / JX997173.1
67 / Ectocarpus siliculosus virus, complete genome / 335593 / 1 / AF204951.2
68 / Ectocarpus siliculosus virus 1, complete genome / 335593 / 1 / NC_002687.1
69 / Enterobacteria phage RB3, complete genome / 333581 / 2 / NC_025419.1
70 / Paramecium bursaria Chlorella virus AN69C, partial genome / 332309 / 1 / JX997153.1
71 / Paramecium bursaria Chlorella virus 1 (PBCV-1), complete genome / 330611 / 1 / JF411744.1
72 / Paramecium bursaria Chlorella virus 1, complete genome / 330611 / 1 / NC_000852.5
73 / Paramecium bursaria Chlorella virus CVR-1, partial genome / 330002 / 1 / JX997164.1
74 / Paramecium bursaria Chlorella virus Can18-4, partial genome / 329890 / 1 / JX997157.1
75 / Paramecium bursaria Chlorella virus NE-JV-4, partial genome / 328315 / 1 / JX997179.1
76 / Acanthocystis turfacea Chlorella virus MN0810.1, partial genome / 327406 / 1 / JX997174.1
77 / Paramecium bursaria Chlorella virus AP110A, partial genome / 327349 / 1 / JX997154.1
78 / Paramecium bursaria Chlorella virus CVM-1, partial genome / 327107 / 1 / JX997163.1
79 / Paramecium bursaria Chlorella virus CVA-1, partial genome / 326592 / 1 / JX997159.1
80 / Paramecium bursaria Chlorella virus NE-JV-1, partial genome / 326559 / 1 / JX997176.1
81 / Paramecium bursaria Chlorella virus NW665.2, partial genome / 325996 / 1 / JX997181.1
82 / Acanthocystis turfacea Chlorella virus NTS-1, partial genome / 323517 / 1 / JX997180.1
83 / Paramecium bursaria Chlorella virus IL-3A, partial genome / 323497 / 1 / JX997169.1
84 / Paramecium bursaria Chlorella virus FR483, complete genome / 321240 / 1 / NC_008603.1
85 / Acanthocystis turfacea Chlorella virus TN603.4.2, partial genome / 320880 / 1 / JX997186.1
86 / Acanthocystis turfacea Chlorella virus NE-JV-2, partial genome / 319583 / 1 / JX997177.1
87 / Paramecium bursaria Chlorella virus CVB-1, partial genome / 319457 / 1 / JX997160.1
88 / Paramecium bursaria Chlorella virus CVG-1, partial genome / 318742 / 1 / JX997161.1
89 / Pseudomonas phage 201phi2-1, complete genome / 316674 / 1 / NC_010821.1
90 / Acanthocystis turfacea Chlorella virus GM0701.1, partial genome / 315239 / 1 / JX997168.1
91 / Paramecium bursaria chlorella virus MT325 genomic sequence / 314335 / 1 / DQ491001.1
92 / Paramecium bursaria Chlorella virus OR0704.2.2, partial genome / 313584 / 1 / JX997184.1
93 / Acanthocystis turfacea Chlorella virus OR0704.3, partial genome / 311647 / 1 / JX997185.1
94 / Paramecium bursaria Chlorella virus CvsA1, partial genome / 311223 / 1 / JX997165.1
95 / Pseudomonas phage PhiPA3, complete genome / 309208 / 1 / HQ630627.1
96 / Paramecium bursaria Chlorella virus CviKI, partial genome / 309195 / 1 / JX997162.1
97 / Choristoneura biennis entomopoxvirus ‘L’, complete genome / 307691 / 1 / NC_021248.1
98 / Penguinpox virus isolate PSan92, complete genome / 306862 / 1 / NC_024446.1
99 / Acanthocystis turfacea Chlorella virus Can0610SP, partial genome / 306752 / 1 / JX997156.1
100 / Paramecium bursaria Chlorella virus CZ-2, partial genome / 305715 / 1 / JX997166.1
101 / White spot syndrome virus, complete genome / 305119 / 1 / AF332093.3
102 / Shrimp white spot syndrome virus, complete genome / 305108 / 1 / NC_003225.2
103 / Sequence 1 from Patent WO0138351 / 305107 / 1 / AX151396.1
104 / Paramecium bursaria Chlorella virus Fr5L, partial genome / 303810 / 1 / JX997167.1
105 / Emiliania huxleyi virus PS401, *** SEQUENCING IN PROGRESS ***, 13 unordered pieces / 301520 / 1 / HQ634146.1

Table S4: The giant viruses found by the “Giant Virus Finder”. DNA sequences found k times in the samples are denoted by ‘k x “name of species”’.

Source description * / Source location and taxa found*
Deserts and xeric shrubland / Lake Bonney Valley, Antarctica
mgm4477803.3.050 / Organic Lake phycodnavirus
Aureococcus anophagefferens virus
Megavirus terra1
Klebsiella phage K64-1
Acanthamoeba polyphaga moumouvirus
Acanthocystis turfacea Chlorella virus
Temperate grasslands / Konza Prairie LTER, Kansas, USA
mgm4477804.3.050 / Samba virus
Pandoravirus salinus
Deserts and xeric shrubland / Mojave Desert, California, USA
mgm4477805.3.050 / 2 x Pandoravirus inopinatum
Pandoravirus salinus
Trop. & subtrop. broadleaf forest / Manu National Park, Peru
mgm4477807.3.050
Deserts and xeric shrubland / Chihuahuan Desert, Galisteo, NM, USA
mgm4477872.3.050 / 2 x Acanthamoeba polyphaga moumouvirus
Ectocarpus siliculosus virus
Moumouvirus Monve
Pandoravirus dulcis
Samba virus
Megavirus lba
Deserts and xeric shrubland / Chihuahuan Desert, Sevilleta, NM, USA
mgm4477873.3.050 / 3 x Megavirus terra1
2 x Megavirus lba
Paramecium bursaria Chlorella virus
Samba virus
Mimivirus terra2
Megavirus courdo11
Tundra / Toolik Lake LTER, Alaska, USA
mgm4477874.3.050 / 2 x Acanthamoeba polyphaga moumouvirus
2 x Cafeteria roenbergensis virus
Megavirus terra1
Trop. & subtrop. broadleaf forest / Misiones, Argentina
mgm4477875.3.050 / Pandoravirus inopinatum
Acanthamoeba polyphaga moumouvirus
Pandoravirus dulcis
Temperate coniferous forest / Bonanza Creek LTER, Alaska, USA
mgm4477876.3.050 / 8 x Megavirus terra1
Paramecium bursaria Chlorella virus
3 x Samba virus
Megavirus lba
Pandoravirus dulcis
Acanthocystis turfacea Chlorella virus
Acanthamoeba polyphaga moumouvirus
Klebsiella phage K64-1
Cronobacter phage vB_CsaM_GAP32
2 x Moumouvirus Monve
Cafeteria roenbergensis virus
Temperate coniferous forest / Calhoun Experimental Forest, SC, USA
mgm4477877.3.050 / Cafeteria roenbergensis virus
Temperate coniferous forest / Duke Forest, North Carolina, USA
mgm4477899.3.050 / Samba virus
Cafeteria roenbergensis virus
Pandoravirus salinus
Pandoravirus dulcis
Deserts and xeric shrubland / Garwood Valley, Antarctica
mgm4477900.3.050 / Mimivirus terra2
Samba virus
Acanthamoeba polyphaga moumouvirus
2 x Cafeteria roenbergensis virus
5 x Megavirus terra1
Megavirus chiliensis
Deserts and xeric shrubland / Lake Bonney Valley, Antarctica
mgm4477901.3.050 / Cronobacter phage PBECO 4
Deserts and xeric shrubland / Lake Fryxell Valley, Antarctica
mgm4477902.3.050 / 3 x Acanthamoeba polyphaga moumouvirus
4 x Megavirus terra1
4 x Pandoravirus inopinatum
Paramecium bursaria Chlorella virus
2 x Cafeteria roenbergensis virus
2 x Moumouvirus Monve
2x Samba virus
2 x Pandoravirus dulcis
2 x Megavirus lba
Deserts and xeric shrubland / Lake Hoare Valley, Antarctica
mgm4477903.3.050 / Pandoravirus dulcis
Pandoravirus salinus
Deserts and xeric shrubland / Wright Valley, Antarctica
mgm4477904.3.050 / Mimivirus terra2
Megavirus terra1
Pandoravirus inopinatum
Pandoravirus salinus
Hirudovirus strain Sangsue
2 x Pandoravirus dulcis
Moumouvirus Monve
Paramecium bursaria Chlorella virus
Acanthamoeba polyphaga moumouvirus