<table><caption>Supplementary Table S1: pooling strategy to generate the viral communities pools of variable complexity (from 5 to 60 viruses</caption><thead><tr><th>60 viruses pool</th><th>20 viruses pools</th><th>10 viruses pools</th><th>5 viruses pools</th><th>Family</th><th>Genus</th></tr></thead><tbody><tr><td rowspan="12">P60</td><td rowspan="12">P20-1</td><td rowspan="5">P10-1</td><td>P5-1</td><td>Bromoviridae<br>Alphaflexiviridae<br>Tombusviridae<br>Partitiviridae<br>Benyviridae</td><td>Alfamovirus<br>Allexivirus<br>Alphacarmovirus<br>Alphacryptovirus<br>Benyvirus</td></tr><tr><td>P5-2</td><td>Tombusviridae<br>Bromoviridae<br>Potyviridae<br>Caulimoviridae<br>Betaflexiviridae</td><td>Alphanecrovirus<br>Anulavirus<br>Bymovirus<br>Badnavirus<br>Capillovirus</td></tr><tr><td>P5-3</td><td>Tombusviridae<br>Geminiviridae<br>Betaflexiviridae<br>Bromoviridae<br>Secoviridae</td><td>Betacarmovirus<br>Begomovirus<br>Carlavirus<br>Bromovirus<br>Cheravirus</td></tr><tr><td>P5-4</td><td>Nanoviridae<br>Tombusviridae<br>Closteroviridae<br>Secoviridae<br>Solemoviridae/Luteoviridae</td><td>Babuvirus<br>Aureusvirus<br>Closterovirus<br>Comovirus<br>Enamovirus/Umbravirus</td></tr><tr><td>P5-5</td><td>Tombusviridae<br>Caulimoviridae<br>Closteroviridae<br>Bromoviridae<br>Virgaviridae</td><td>Betanecrovirus<br>Caulimovirus<br>Crinivirus<br>Cucumovirus<br>Furovirus</td></tr><tr><td rowspan="4">P10-2</td><td>P5-6</td><td>Rhabdoviridae<br>Tombusviridae<br>Secoviridae<br>Not assigned<br>Virgaviridae</td><td>Cytorhabdovirus<br>Dianthovirus<br>Fabavirus<br>Idaeovirus<br>Hordeivirus</td></tr><tr><td>P5-7</td><td>Tombusviridae<br>Bromoviridae<br>Potyviridae<br>Rhabdoviridae<br>Tombusviridae</td><td>Gammacarmovirus<br>Ilarvirus<br>Ipomovirus<br>Varicosavirus<br>Machlomovirus</td></tr><tr><td>P5-8</td><td>Geminiviridae<br>Secoviridae<br>Luteoviridae<br>Virgaviridae<br>Betaflexiviridae</td><td>Mastrevirus<br>Nepovirus<br>Polerovirus<br>Pomovirus<br>Trichovirus</td></tr><tr><td>P5-9</td><td>Virgaviridae<br>Tombusviridae<br>Alphaflexiviridae<br>Potyviridae<br>Rhabdoviridae</td><td>Pecluvirus<br>Pelarspovirus<br>Potexvirus<br>Potyvirus<br>Alphanucleorhabdovirus</td></tr><tr><td rowspan="4">P10-3</td><td>P5-10</td><td>Rhabdoviridae<br>Potyviridae<br>Secoviridae<br>Solemoviridae<br>Betaflexiviridae</td><td>Betanucleorhabdovirus<br>Rymovirus<br>Sequivirus<br>Sobemovirus<br>Tepovirus</td></tr><tr><td>P5-11</td><td>Aspiviridae<br>Virgaviridae<br>Tombusviridae<br>Potyviridae<br>Tymoviridae</td><td>Ophiovirus<br>Tobravirus<br>Tombusvirus<br>Tritimovirus<br>Tymovirus</td></tr><tr><td>P5-12</td><td>Virgaviridae<br>Secoviridae<br>Tombusviridae<br>Potyviridae<br>Tospoviridae</td><td>Tobamovirus<br>unassigned<br>Umbravirus<br>unassigned<br>Orthotospovirus</td></tr><tr><td>P10-4</td><td></td><td></td></tr><tr><td rowspan="12">P20-2</td><td rowspan="12">P20-2</td><td rowspan="5">P10-5</td><td>P5-1</td><td>Bromoviridae<br>Alphaflexiviridae<br>Tombusviridae<br>Partitiviridae<br>Benyviridae</td><td>Alfamovirus<br>Allexivirus<br>Alphacarmovirus<br>Alphacryptovirus<br>Benyvirus</td></tr><tr><td>P5-2</td><td>Tombusviridae<br>Bromoviridae<br>Potyviridae<br>Caulimoviridae<br>Betaflexiviridae</td><td>Alphanecrovirus<br>Anulavirus<br>Bymovirus<br>Badnavirus<br>Capillovirus</td></tr><tr><td>P5-3</td><td>Tombusviridae<br>Geminiviridae<br>Betaflexiviridae<br>Bromoviridae<br>Secoviridae</td><td>Betacarmovirus<br>Begomovirus<br>Carlavirus<br>Bromovirus<br>Cheravirus</td></tr><tr><td>P5-4</td><td>Nanoviridae<br>Tombusviridae<br>Closteroviridae<br>Secoviridae<br>Solemoviridae/Luteoviridae</td><td>Babuvirus<br>Aureusvirus<br>Closterovirus<br>Comovirus<br>Enamovirus/Umbravirus</td></tr><tr><td>P5-5</td><td>Tombusviridae<br>Caulimoviridae<br>Closteroviridae<br>Bromoviridae<br>Virgaviridae</td><td>Betanecrovirus<br>Caulimovirus<br>Crinivirus<br>Cucumovirus<br>Furovirus</td></tr><tr><td rowspan="4">P10-6</td><td>P5-6</td><td>Rhabdoviridae<br>Tombusviridae<br>Secoviridae<br>Not assigned<br>Virgaviridae</td><td>Cytorhabdovirus<br>Dianthovirus<br>Fabavirus<br>Idaeovirus<br>Hordeivirus</td></tr><tr><td>P5-7</td><td>Tombusviridae<br>Bromoviridae<br>Potyviridae<br>Rhabdoviridae<br>Tombusviridae</td><td>Gammacarmovirus<br>Ilarvirus<br>Ipomovirus<br>Varicosavirus<br>Machlomovirus</td></tr><tr><td>P5-8</td><td>Geminiviridae<br>Secoviridae<br>Luteoviridae<br>Virgaviridae<br>Betaflexiviridae</td><td>Mastrevirus<br>Nepovirus<br>Polerovirus<br>Pomovirus<br>Trichovirus</td></tr><tr><td>P5-9</td><td>Virgaviridae<br>Tombusviridae<br>Alphaflexiviridae<br>Potyviridae<br>Rhabdoviridae</td><td>Pecluvirus<br>Pelarspovirus<br>Potexvirus<br>Potyvirus<br>Alphanucleorhabdovirus</td></tr><tr><td rowspan="4">P10-3</td><td>P5-10</td><td>Rhabdoviridae<br>Potyviridae<br>Secoviridae<br>Solemoviridae<br>Betaflexiviridae</td><td>Betanucleorhabdovirus<br>Rymovirus<br>Sequivirus<br>Sobemovirus<br>Tepovirus</td></tr><tr><td>P5-11</td><td>Aspiviridae<br>Virgaviridae<br>Tombusviridae<br>Potyviridae<br>Tymoviridae</td><td>Ophiovirus<br>Tobravirus<br>Tombusvirus<br>Tritimovirus<br>Tymovirus</td></tr><tr><td>P5-12</td><td>Virgaviridae<br>Secoviridae<br>Tombusviridae<br>Potyviridae<br>Tospoviridae</td><td>Tobamovirus<br>unassigned<br>Umbravirus<br>unassigned<br>Orthotospovirus</td></tr><tr><td>P10-4</td><td></td><td></td></tr></tbody></table>
<table><caption>Supplementary Table S1: pooling strategy to generate the viral communities pools of variable complexity (from 5 to 60 viruses</caption><thead><tr><th>60 viruses pool</th><th>20 viruses pools</th><th>10 viruses pools</th><th>5 viruses pools</th><th>Family</th><th>Genus</th></tr></thead><tbody><tr><td rowspan="12">P60</td><td rowspan="12">P20-1</td><td rowspan="5">P10-1</td><td>P5-1</td><td>Bromoviridae<br>Alphaflexiviridae<br>Tombusviridae<br>Partitiviridae<br>Benyviridae</td><td>Alfamovirus<br>Allexivirus<br>Alphacarmovirus<br>Alphacryptovirus<br>Benyvirus</td></tr><tr><td>P5-2</td><td>Tombusviridae<br>Bromoviridae<br>Potyviridae<br>Caulimoviridae<br>Betaflexiviridae</td><td>Alphanecrovirus<br>Anulavirus<br>Bymovirus<br>Badnavirus<br>Capillovirus</td></tr><tr><td>P5-3</td><td>Tombusviridae<br>Geminiviridae<br>Betaflexiviridae<br>Bromoviridae<br>Secoviridae</td><td>Betacarmovirus<br>Begomovirus<br>Carlavirus<br>Bromovirus<br>Cheravirus</td></tr><tr><td>P5-4</td><td>Nanoviridae<br>Tombusviridae<br>Closteroviridae<br>Secoviridae<br>Solemoviridae/Luteoviridae</td><td>Babuvirus<br>Aureusvirus<br>Closterovirus<br>Comovirus<br>Enamovirus/Umbravirus</td></tr><tr><td>P5-5</td><td>Tombusviridae<br>Caulimoviridae<br>Closteroviridae<br>Bromoviridae<br>Virgaviridae</td><td>Betanecrovirus<br>Caulimovirus<br>Crinivirus<br>Cucumovirus<br>Furovirus</td></tr><tr><td rowspan="5">P10-2</td><td>P5-6</td><td>Rhabdoviridae<br>Tombusviridae<br>Secoviridae<br>Not assigned<br>Virgaviridae</td><td>Cytorhabdovirus<br>Dianthovirus<br>Fabavirus<br>Idaeovirus<br>Hordeivirus</td></tr><tr><td>P5-7</td><td>Tombusviridae<br>Bromoviridae<br>Potyviridae<br>Rhabdoviridae<br>Tombusviridae</td><td>Gammacarmovirus<br>Ilarvirus<br>Ipomovirus<br>Varicosavirus<br>Machlomovirus</td></tr><tr><td>P5-8</td><td>Geminiviridae<br>Secoviridae<br>Luteoviridae<br>Virgaviridae<br>Betaflexiviridae</td><td>Mastrevirus<br>Nepovirus<br>Polerovirus<br>Pomovirus<br>Trichovirus</td></tr><tr><td>P5-9</td><td>Virgaviridae<br>Tombusviridae<br>Alphaflexiviridae<br>Potyviridae<br>Rhabdoviridae</td><td>Pecluvirus<br>Pelarspovirus<br>Potexvirus<br>Potyvirus<br>Alphanucleorhabdovirus</td></tr><tr><td>P5-10</td><td>Rhabdoviridae<br>Potyviridae<br>Secoviridae<br>Solemoviridae<br>Betaflexiviridae</td><td>Betanucleorhabdovirus<br>Rymovirus<br>Sequivirus<br>Sobemovirus<br>Tepovirus</td></tr><tr><td rowspan="5">P20-2</td><td rowspan="5">P10-3</td><td>P5-11</td><td>Aspiviridae<br>Virgaviridae<br>Tombusviridae<br>Potyviridae<br>Tymoviridae</td><td>Ophiovirus<br>Tobravirus<br>Tombusvirus<br>Tritimovirus<br>Tymovirus</td></tr><tr><td>P5-12</td><td>Virgaviridae<br>Secoviridae<br>Tombusviridae<br>Potyviridae<br>Tospoviridae</td><td>Tobamovirus<br>unassigned<br>Umbravirus<br>unassigned<br>Orthotospovirus</td></tr><tr><td>P5-13</td><td>Aspiviridae<br>Virgaviridae<br>Tombusviridae<br>Potyviridae<br>Tymoviridae</td><td>Ophiovirus<br>Tobravirus<br>Tombusvirus<br>Tritimovirus<br>Tymovirus</td></tr><tr><td>P5-14</td><td>Virgaviridae<br>Secoviridae<br>Tombusviridae<br>Potyviridae<br>Tospoviridae</td><td>Tobamovirus<br>unassigned<br>Umbravirus<br>unassigned<br>Orthotospovirus</td></tr><tr><td>P5-15</td><td>Aspiviridae<br>Virgaviridae<br>Tombusviridae<br>Potyviridae<br>Tymoviridae</td><td>Ophiovirus<br>Tobravirus<br>Tombusvirus<br>Tritimovirus<br>Tymovirus</td></tr></tbody></table>
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<table><thead><tr><td>Virus species</td><td>Genome type</td></tr></thead><tbody><tr><td>Alfalfa mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Shallot virus X</td><td>ssRNA(+)</td></tr><tr><td>Calibrachoa mottle Virus</td><td>ssRNA(+)</td></tr><tr><td>Poinsettia latent virus</td><td>dsRNA</td></tr><tr><td>Beet necrotic yellow vein virus</td><td>ssRNA(+)</td></tr><tr><td>Tobacco necrosis virus A</td><td>ssRNA(+)</td></tr><tr><td>Pelargonium zonate spot virus</td><td>ssRNA(+)</td></tr><tr><td>Barley yellow mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Banana streak OL virus</td><td>dsDNA-RT</td></tr><tr><td>Apple stem grooving virus</td><td>ssRNA(+)</td></tr><tr><td>Turnip crinkle virus</td><td>ssRNA(+)</td></tr><tr><td>Squash leaf curl virus</td><td>ssDNA</td></tr><tr><td>Poplar mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Brome mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Arracacha virus B</td><td>ssRNA(+)</td></tr><tr><td>Banana bunchy top virus</td><td>ssDNA</td></tr><tr><td>Johnsongrass chlorotic stripe mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Beet yellows virus</td><td>ssRNA(+)</td></tr><tr><td>Squash mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Pea enation mosaic virus 1 and 2</td><td>ssRNA(+)</td></tr><tr><td>Beet black scorch virus</td><td>ssRNA(+)</td></tr><tr><td>Cauliflower mosaic virus</td><td>dsDNA-RT</td></tr><tr><td>Tomato chlorosis virus</td><td>ssRNA(+)</td></tr><tr><td>Peanut stunt virus</td><td>ssRNA(+)</td></tr><tr><td>Soil-borne wheat mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Lettuce necrotic yellows virus</td><td>ssRNA(-)</td></tr><tr><td>Carnation ringspot virus</td><td>ssRNA(+)</td></tr><tr><td>Broad bean wilt virus 1</td><td>ssRNA(+)</td></tr><tr><td>Raspberry bushy dwarf virus</td><td>ssRNA(+)</td></tr><tr><td>Barley stripe mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Melon necrotic spot virus</td><td>ssRNA(+)</td></tr><tr><td>Parietaria mottle virus</td><td>ssRNA(+)</td></tr><tr><td>Cucumber vein yellowing virus</td><td>ssRNA(+)</td></tr><tr><td>Beet oak leaf virus</td><td>ssRNA(-)</td></tr><tr><td>Maize chlorotic mottle virus</td><td>ssRNA(+)</td></tr><tr><td>Maize streak virus</td><td>ssDNA</td></tr><tr><td>Tomato black ring virus</td><td>ssRNA(+)</td></tr><tr><td>Cucurbit aphid-borne yellows virus</td><td>ssRNA(+)</td></tr><tr><td>Potato mop-top virus</td><td>ssRNA(+)</td></tr><tr><td>Apple chlorotic leaf spot virus</td><td>ssRNA(+)</td></tr><tr><td>Peanut clump virus</td><td>ssRNA(+)</td></tr><tr><td>Pelargonium line pattern virus</td><td>ssRNA(+)</td></tr><tr><td>Lettuce virus X</td><td>ssRNA(+)</td></tr><tr><td>Bidens mottle virus</td><td>ssRNA(+)</td></tr><tr><td>Physostegia chlorotic mottle virus</td><td>ssRNA(-)</td></tr><tr><td>Sonchus yellow net virus</td><td>ssRNA(-)</td></tr><tr><td>Agropyron mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Carrot necrotic dieback virus</td><td>ssRNA(+)</td></tr><tr><td>Rice yellow mottle virus</td><td>ssRNA(+)</td></tr><tr><td>Potato virus T</td><td>ssRNA(+)</td></tr><tr><td>Lettuce ring necrosis virus</td><td>ssRNA(-)</td></tr><tr><td>Pea early-browning virus</td><td>ssRNA(+)</td></tr><tr><td>Tomato bushy stunt virus</td><td>ssRNA(+)</td></tr><tr><td>Brome streak mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Turnip yellow mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Paprika mild mottle virus</td><td>ssRNA(+)</td></tr><tr><td>Strawberry latent ringspot virus</td><td>ssRNA(+)</td></tr><tr><td>Carrot mottle virus</td><td>ssRNA(+)</td></tr><tr><td>Spartina mottle virus</td><td>ssRNA(+)</td></tr><tr><td>Impatiens necrotic spot virus</td><td>ssRNA(+/-)</td></tr></tbody></table>
s in a pool)

<table><thead><tr><td>Virus species</td><td>Genome type</td></tr></thead><tbody><tr><td>Alfalfa mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Shallot virus X</td><td>ssRNA(+)</td></tr><tr><td>Calibrachoa mottle Virus</td><td>ssRNA(+)</td></tr><tr><td>Poinsettia latent virus</td><td>dsRNA</td></tr><tr><td>Beet necrotic yellow vein virus</td><td>ssRNA(+)</td></tr><tr><td>Tobacco necrosis virus A</td><td>ssRNA(+)</td></tr><tr><td>Pelargonium zonate spot virus</td><td>ssRNA(+)</td></tr><tr><td>Barley yellow mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Banana streak OL virus</td><td>dsDNA-RT</td></tr><tr><td>Apple stem grooving virus</td><td>ssRNA(+)</td></tr><tr><td>Turnip crinkle virus</td><td>ssRNA(+)</td></tr><tr><td>Squash leaf curl virus</td><td>ssDNA</td></tr><tr><td>Poplar mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Brome mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Arracacha virus B</td><td>ssRNA(+)</td></tr><tr><td>Banana bunchy top virus</td><td>ssDNA</td></tr><tr><td>Johnsongrass chlorotic stripe mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Beet yellows virus</td><td>ssRNA(+)</td></tr><tr><td>Squash mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Pea enation mosaic virus 1 and 2</td><td>ssRNA(+)</td></tr><tr><td>Beet black scorch virus</td><td>ssRNA(+)</td></tr><tr><td>Cauliflower mosaic virus</td><td>dsDNA-RT</td></tr><tr><td>Tomato chlorosis virus</td><td>ssRNA(+)</td></tr><tr><td>Peanut stunt virus</td><td>ssRNA(+)</td></tr><tr><td>Soil-borne wheat mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Lettuce necrotic yellows virus</td><td>ssRNA(-)</td></tr><tr><td>Carnation ringspot virus</td><td>ssRNA(+)</td></tr><tr><td>Broad been wilt virus 1</td><td>ssRNA(+)</td></tr><tr><td>Raspberry bushy dwarf virus</td><td>ssRNA(+)</td></tr><tr><td>Barley stripe mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Melon necrotic spot virus</td><td>ssRNA(+)</td></tr><tr><td>Parietaria mottle virus</td><td>ssRNA(+)</td></tr><tr><td>Cucumber vein yellowing virus</td><td>ssRNA(+)</td></tr><tr><td>Beet oak leaf virus</td><td>ssRNA(-)</td></tr><tr><td>Maize chlorotic mottle virus</td><td>ssRNA(+)</td></tr><tr><td>Maize streak virus</td><td>ssDNA</td></tr><tr><td>Tomato black ring virus</td><td>ssRNA(+)</td></tr><tr><td>Cucurbit aphid-borne yellows virus</td><td>ssRNA(+)</td></tr><tr><td>Potato mop-top virus</td><td>ssRNA(+)</td></tr><tr><td>Apple chlorotic leaf spot virus</td><td>ssRNA(+)</td></tr><tr><td>Peanut clump virus</td><td>ssRNA(+)</td></tr><tr><td>Pelargonium line pattern virus</td><td>ssRNA(+)</td></tr><tr><td>Lettuce virus X</td><td>ssRNA(+)</td></tr><tr><td>Bidens mottle virus</td><td>ssRNA(+)</td></tr><tr><td>Physostegia chlorotic mottle virus</td><td>ssRNA(-)</td></tr><tr><td>Sonchus yellow net virus</td><td>ssRNA(-)</td></tr><tr><td>Agropyron mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Carrot necrotic dieback virus</td><td>ssRNA(+)</td></tr><tr><td>Rice yellow mottle virus</td><td>ssRNA(+)</td></tr><tr><td>Potato virus T</td><td>ssRNA(+)</td></tr><tr><td>Lettuce ring necrosis virus</td><td>ssRNA(-)</td></tr><tr><td>Pea early-browning virus</td><td>ssRNA(+)</td></tr><tr><td>Tomato bushy stunt virus</td><td>ssRNA(+)</td></tr><tr><td>Brome streak mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Turnip yellow mosaic virus</td><td>ssRNA(+)</td></tr><tr><td>Paprika mild mottle virus</td><td>ssRNA(+)</td></tr><tr><td>Strawberry latent ringspot virus</td><td>ssRNA(+)</td></tr><tr><td>Carrot mottle virus</td><td>ssRNA(+)</td></tr><tr><td>Spartina mottle virus</td><td>ssRNA(+)</td></tr><tr><td>Impatiens necrotic spot virus</td><td>ssRNA(+/-)</td></tr></tbody></table>
<table><caption>**Supplementary Table S2.** Comparison of *de novo* assembly parameters for VANA and dsRNA datasets normalized at different sequencing depths (100K, 300K, 1M, 3M and 10M reads, 5 resamplings at each depth) and corresponding statistical significance.</caption><thead><tr><th></th><th></th><th>VANA average +/- SD</th><th>dsRNA average +/- SD</th><th>Two sample t-test</th></tr></thead><tbody><tr><td rowspan="6">100K reads</td><td>nb contigs</td><td>33.6 +/- 1.9</td><td>103.2 +/- 2.4</td><td>2.6E-11</td></tr><tr><td>average length</td><td>733.4 +/- 23.7</td><td>741.8 +/- 14.9</td><td>0.52</td></tr><tr><td>N50</td><td>839.2 +/- 104.8</td><td>937.2 +/- 34.1</td><td>0.10</td></tr><tr><td>Max length</td><td>5886.2 +/- 442.4</td><td>5277.2 +/- 577.9</td><td>0.10</td></tr><tr><td>nb viral contigs</td><td>33.6 +/- 1.9</td><td>101.8 +/- 2.9</td><td>9.2E-11</td></tr><tr><td>% viral contigs</td><td>100% +/- 0%</td><td>99% +/- 1%</td><td>2.5E-02</td></tr><tr><td></td><td>Viral contigs average length</td><td>733.4 +/- 23.7</td><td>747.4 +/- 17.1</td><td>0.32</td></tr><tr><td rowspan="6">300K reads</td><td>nb contigs</td><td>70.6 +/- 6.1</td><td>140.4 +/- 8.9</td><td>5.1E-07</td></tr><tr><td>average length</td><td>642.4 +/- 30.0</td><td>849.4 +/- 35.3</td><td>8.5E-06</td></tr><tr><td>N50</td><td>681.2 +/- 93.1</td><td>1102.4 +/- 104.5</td><td>1.5E-04</td></tr><tr><td>Max length</td><td>6260 +/- 213.1</td><td>7581.6 +/- 3875.5</td><td>0.49</td></tr><tr><td>nb viral contigs</td><td>70.2 +/- 5.4</td><td>129.4 +/- 8.1</td><td>8.0E-07</td></tr><tr><td>% viral contigs</td><td>100% +/- 1%</td><td>92% +/- 2%</td><td>7.7E-05</td></tr><tr><td></td><td>Viral contigs average length</td><td>643.4 +/- 27.8</td><td>887.8 +/- 38.2</td><td>2.8E-06</td></tr><tr><td rowspan="6">1M reads</td><td>nb contigs</td><td>108.2 +/- 6.1</td><td>198.4 +/- 7.8</td><td>3.5E-08</td></tr><tr><td>average length</td><td>687.6 +/- 28.1</td><td>915.4 +/- 35.4</td><td>3.5E-06</td></tr><tr><td>N50</td><td>767 +/- 74.9</td><td>1556.4 +/- 178.3</td><td>2.6E-04</td></tr><tr><td>Max length</td><td>6491 +/- 79.4</td><td>10382.6 +/- 1825.7</td><td>8.9E-03</td></tr><tr><td>nb viral contigs</td><td>106.2 +/- 6.3</td><td>159.2 +/- 6.6</td><td>1.1E-06</td></tr><tr><td>% viral contigs</td><td>98% +/- 1%</td><td>80% +/- 2%</td><td>8.3E-08</td></tr><tr><td></td><td>Viral contigs average length</td><td>694.8 +/- 30.3</td><td>1019.6 +/- 40.9</td><td>5.7E-07</td></tr><tr><td rowspan="6">3M reads</td><td>nb contigs</td><td>134.2 +/- 3.4</td><td>284 +/- 8.2</td><td>2.5E-07</td></tr><tr><td>average length</td><td>783.4 +/- 10.1</td><td>931 +/- 16.6</td><td>1.5E-07</td></tr><tr><td>N50</td><td>1016.6 +/- 73.5</td><td>1599.4 +/- 214.1</td><td>4.3E-04</td></tr><tr><td>Max length</td><td>6540 +/- 3.4</td><td>11573.4 +/- 2359.2</td><td>8.8E-03</td></tr><tr><td>nb viral contigs</td><td>129.6 +/- 4.8</td><td>207.6 +/- 3.8</td><td>2.5E-09</td></tr><tr><td>% viral contigs</td><td>97% +/- 1%</td><td>73% +/- 1%</td><td>1.0E-09</td></tr><tr><td></td><td>Viral contigs average length</td><td>798.4 +/- 15.9</td><td>1067.6 +/- 11.5</td><td>1.4E-09</td></tr><tr><td rowspan="6">10M reads</td><td>nb contigs</td><td>217 +/- 4.4</td><td>433.8 +/- 4.4</td><td>8.2E-13</td></tr><tr><td>average length</td><td>764.6 +/- 10.5</td><td>907.2 +/- 7.7</td><td>8.2E-09</td></tr><tr><td>N50</td><td>1025.4 +/- 31.2</td><td>1529.6 +/- 21.7</td><td>1.8E-09</td></tr><tr><td>Max length</td><td>6534.4 +/- 210.2</td><td>13930.4 +/- 24.9</td><td>1.6E-07</td></tr><tr><td>nb viral contigs</td><td>201.2 +/- 4.1</td><td>268 +/- 2.9</td><td>1.8E-09</td></tr><tr><td>% viral contigs</td><td>93% +/- 0%</td><td>62% +/- 1%</td><td>2.2E-13</td></tr><tr><td></td><td>Viral contigs average length</td><td>791.2 +/- 11.1</td><td>1121.4 +/- 10.6</td><td>3.9E-11</td></tr></tbody></table>
<table><caption>**Supplementary Table S2.** Comparison of *de novo* assembly parameters for VANA and dsRNA datasets normalized at different sequencing depths (100K, 300K, 1M, 3M and 10M reads, 5 resamplings at each depth) and corresponding statistical significance.</caption><thead><tr><th></th><th></th><th>VANA average +/- SD</th><th>dsRNA average +/- SD</th><th>Two sample t-test</th></tr></thead><tbody><tr><td rowspan="6">100K reads</td><td>nb contigs</td><td>33.6 +/- 1.9</td><td>103.2 +/- 2.4</td><td>2.6E-11</td></tr><tr><td>average length</td><td>733.4 +/- 23.7</td><td>741.8 +/- 14.9</td><td>0.52</td></tr><tr><td>N50</td><td>839.2 +/- 104.8</td><td>937.2 +/- 34.1</td><td>0.10</td></tr><tr><td>Max length</td><td>5886.2 +/- 442.4</td><td>5277.2 +/- 577.9</td><td>0.10</td></tr><tr><td>nb viral contigs</td><td>33.6 +/- 1.9</td><td>101.8 +/- 2.9</td><td>9.2E-11</td></tr><tr><td>% viral contigs</td><td>100% +/- 0%</td><td>99% +/- 1%</td><td>2.5E-02</td></tr><tr><td></td><td>Viral contigs average length</td><td>733.4 +/- 23.7</td><td>747.4 +/- 17.1</td><td>0.32</td></tr><tr><td rowspan="6">300K reads</td><td>nb contigs</td><td>70.6 +/- 6.1</td><td>140.4 +/- 8.9</td><td>5.1E-07</td></tr><tr><td>average length</td><td>642.4 +/- 30.0</td><td>849.4 +/- 35.3</td><td>8.5E-06</td></tr><tr><td>N50</td><td>681.2 +/- 93.1</td><td>1102.4 +/- 104.5</td><td>1.5E-04</td></tr><tr><td>Max length</td><td>6260 +/- 213.1</td><td>7581.6 +/- 3875.5</td><td>0.49</td></tr><tr><td>nb viral contigs</td><td>70.2 +/- 5.4</td><td>129.4 +/- 8.1</td><td>8.0E-07</td></tr><tr><td>% viral contigs</td><td>100% +/- 1%</td><td>92% +/- 2%</td><td>7.7E-05</td></tr><tr><td></td><td>Viral contigs average length</td><td>643.4 +/- 27.8</td><td>887.8 +/- 38.2</td><td>2.8E-06</td></tr><tr><td rowspan="6">1M reads</td><td>nb contigs</td><td>108.2 +/- 6.1</td><td>198.4 +/- 7.8</td><td>3.5E-08</td></tr><tr><td>average length</td><td>687.6 +/- 28.1</td><td>915.4 +/- 35.4</td><td>3.5E-06</td></tr><tr><td>N50</td><td>767 +/- 74.9</td><td>1556.4 +/- 178.3</td><td>2.6E-04</td></tr><tr><td>Max length</td><td>6491 +/- 79.4</td><td>10382.6 +/- 1825.7</td><td>8.9E-03</td></tr><tr><td>nb viral contigs</td><td>106.2 +/- 6.3</td><td>159.2 +/- 6.6</td><td>1.1E-06</td></tr><tr><td>% viral contigs</td><td>98% +/- 1%</td><td>80% +/- 2%</td><td>8.3E-08</td></tr><tr><td></td><td>Viral contigs average length</td><td>694.8 +/- 30.3</td><td>1019.6 +/- 40.9</td><td>5.7E-07</td></tr><tr><td rowspan="6">3M reads</td><td>nb contigs</td><td>134.2 +/- 3.4</td><td>284 +/- 8.2</td><td>2.5E-07</td></tr><tr><td>average length</td><td>783.4 +/- 10.1</td><td>931 +/- 16.6</td><td>1.5E-07</td></tr><tr><td>N50</td><td>1016.6 +/- 73.5</td><td>1599.4 +/- 214.1</td><td>4.3E-04</td></tr><tr><td>Max length</td><td>6540 +/- 3.4</td><td>11573.4 +/- 2359.2</td><td>8.8E-03</td></tr><tr><td>nb viral contigs</td><td>129.6 +/- 4.8</td><td>207.6 +/- 3.8</td><td>2.5E-09</td></tr><tr><td>% viral contigs</td><td>97% +/- 1%</td><td>73% +/- 1%</td><td>1.0E-09</td></tr><tr><td></td><td>Viral contigs average length</td><td>798.4 +/- 15.9</td><td>1067.6 +/- 11.5</td><td>1.4E-09</td></tr><tr><td rowspan="6">10M reads</td><td>nb contigs</td><td>217 +/- 4.4</td><td>433.8 +/- 4.4</td><td>8.2E-13</td></tr><tr><td>average length</td><td>764.6 +/- 10.5</td><td>907.2 +/- 7.7</td><td>8.2E-09</td></tr><tr><td>N50</td><td>1025.4 +/- 31.2</td><td>1529.6 +/- 21.7</td><td>1.8E-09</td></tr><tr><td>Max length</td><td>6534.4 +/- 210.2</td><td>13930.4 +/- 24.9</td><td>1.6E-07</td></tr><tr><td>nb viral contigs</td><td>201.2 +/- 4.1</td><td>268 +/- 2.9</td><td>1.8E-09</td></tr><tr><td>% viral contigs</td><td>93% +/- 0%</td><td>62% +/- 1%</td><td>2.2E-13</td></tr><tr><td></td><td>Viral contigs average length</td><td>791.2 +/- 11.1</td><td>1121.4 +/- 10.6</td><td>3.9E-11</td></tr></tbody></table>