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Table 2 Assembly of Mengovirus and MIDV genomes with different assembler software with targeted and untargeted sequences obtained after selection using similarity-based approach

From: Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data

  ArTB 5290 ArB 19017 AnrB 3741
Targeted Untargeted Targeted Untargeted Targeted Untargeted
ABYSS Contigs (≥50 bp) 2463 11,822 24 20,618 15 5905
Contigs (≥1000 bp) 3 0 2 0 1 0
Largest contig 1807 372 3219 195 7025 266
Mean length 88 84 576 82 392 82
N50 1185 124 2574 124 7025 124
L50 3 1501 1 2218 1 599
Ray Contigs (≥50 bp) 2 35 3 12 4 28
Contigs (≥1000 bp) 2 0 2 2 2 0
Largest contig 6906 837 4088 1873 4360 552
Mean length 4844 284 2013 210 2571 523
N50 6906 575 4088 1102 3745 552
L50 1 2 1 2 1 1
SPAdes v3.0 Contigs (≥50 bp) 2 371 1 16 1 322
Contigs (≥1000 bp) 1 2 1 2 1 0
Largest contig 11,468 1065 7548 3492 7562 951
Mean length 5789 145 7562 127 7548 110
N50 11,468 892 7548 3492 7562 951
L50 1 3 1 1 1 1
SPAdes v3.5/SPAdes v3.6 Contigs (≥50 bp) 5 10,435 7 569 2 322
Contigs (≥1000 bp) 1 0 1 0 1 0
Largest contig 11,314 331 7548 396 7548 951
Mean length 2359 100 3896 127 1174 110
N50 11,314 129 7548 141 7548 951
L50 1 2492 1 113 1 1
  1. The reads whose regions of the viral sequences were selected within the reads were named «Targeted Sequences» or TS, whereas the untreated sequences were named «Untargeted Sequences» or US