The effect of variant interference on de novo assembly for viral deep sequencing

Christina J. Castro; Rachel L. Marine; Edward Ramos; Terry Fei Fan Ng

The rise of NGS and de novo assembler use in GenBank viral sequences 73 74 GenBank viral entries from 1982-2017 were collected and analyzed, with extensive analyses performed 75 to evaluate technologies and bioinformatics programs cited in records deposited between 2011 and 2017. 76 Through 2017, there were over 2.3 million viral entries in GenBank; however, over 70% (1.7 million) do not 77 specify a sequencing technology [Supplement Table S1 ] due to the looser data requirement in earlier years. 78 When looking at recently deposited records (2014) (2015) (2016) (2017) , the Illumina sequencing platform was the most 79 common NGS platform used for viral sequencing, with about a 2-fold increase over the next most popular NGS 80 platform [ Figure 1d & e]. When long sequences (≥2,000 nt) are considered, NGS technologies surpassed 81 Sanger in 2017 as the dominant strategy for sequencing, comprising 53.8% (14,653/27,217) of entries 82 compared to 46.2% of entries (12,564/27,217) for Sanger [ Figure 1f and Supplement Table S2 ]. 83 84 Hybrid sequencing approaches, where researchers use more than one sequencing technology to 85 generate complete viral sequences, have also become more common over the past several years. The most 86 common combination observed was 454 and Sanger (18,002 entries), likely due to the early emergence of the 87 454 technology compared to other NGS platforms [ Figure 1c and Supplement Table S3 ]. However, combining 88 Illumina with various other sequencing platforms is quite commonplace (>10,000 entries).