1. Next Generation Sequencing, Alignment on Databases (Bioinformatics for Infectious Diseases)

Bioinformatics for Infectious Diseases
Next Generation Sequencing, Alignment on Databases (May 4th, 2020)

Next-generation sequencing data analysis: Identification of Viral Genomes in Host Transcriptome or any other kind of fastq files with short reads

~Overview of NGS: reads, sequences, file formats
~Alignment, annotation and non-mapped reads
~Alignment to databases of viral genomes

[marwanmahmoodsaleh]

Hello
I had done the whole genome sequence by NGS (Illumina) of the bacteria. The files I received from the company are Fastaq1, Fastaq2, Filtered 1 Fastq Filtered 2 Fastq and analysis results file include :rmdup.bam.bai, rmdup.bam, filtered vcf and annotated vcf. Please tell me which of these files should be converted to FASTA and submitted to NCBI? Thanks