Clc sequence viewer vs geneious verification#

Clc sequence viewer vs geneious verification#

The MOCV1 genome was used as a reference genome for the annotation of the newly sequenced isolate using Geneious version 10.2.2, and further verification of the predicted open reading frames (ORFs) longer than 50 amino acids was performed using CLC Genomics Workbench version 9.5.4. This resulted in the generation of a 185,655-bp genome, including two inverted terminal repeats, each 2,505 bp long with a G+C content of 62%, and an average coverage of 404.20×. The draft genome sequence was further checked by mapping with a reference MOCV1 genome (GenBank accession no. The resulting contig was further checked and validated by mapping back the trimmed reads. This yielded a single contig of 185,602 bp. Unmapped reads were used as input data for de novo assembly using the SPAdes assembler version 3.10.1 ( 14). GCF_000001405.26) to remove host DNA contamination. A total of 4,695,968 raw reads were preprocessed to remove adapters, ambiguous base calls, and poor-quality reads, followed by mapping against the human genome ( Homo sapiens GRCh38, GenBank accession no. The sequence data were processed using Geneious version 10.2.2 and CLC Genomics Workbench version 9.5.4 as previously described ( 12, 13). Cluster generation and sequencing were performed using a MiSeq reagent kit version 3, generating 301-bp paired-end reads, as described previously ( 10, 11). The quality and quantity of the prepared library were assessed using an Agilent TapeStation system by the Genomic Platform, La Trobe University. The library preparation was conducted with 1 ng of total gDNA using the Illumina Nextera XT DNA library prep kit, as reported previously ( 8, 9). Histologically MOCV-diagnosed formalin-fixed paraffin-embedded (FFPE) cutaneous tissue was aseptically sectioned, and total genomic DNA (gDNA) was extracted using a QIAamp DNA-FFPE tissue kit (Qiagen, USA). The cutaneous tissue sample was collected from the left-hand side of the nose of a 39-year-old woman in 2017.