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Update README.md
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Krithika-Bhuvan authored Mar 2, 2023
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Expand Up @@ -32,7 +32,7 @@ viGEN is a bioinformatics pipeline for the exploration of viral RNA in human NGS
This workflow is part of “Module 1 (filtered human input files)” in Figure 1 in the viGEN manuscript .

### Create viral reference
- We were interested in exploring all viruses existing in humans. So we first obtained reference genomes of all known and sequenced human viruses obtained from NCBI (as of Sep 2015), and merged them into one file (referred to as the "viral reference file") in fasta file format. Merge all virus fasta file into one big fasta file called `viruses.fa` . For this tutorial, we have provided this file through google drive [**here**](https://drive.google.com/drive/folders/0B3-883ME4sP3Wm1FVjdVcEpfek0?usp=sharing).
- We were interested in exploring all viruses existing in humans. So we first obtained reference genomes of all known and sequenced human viruses obtained from NCBI (746 viruses as of Sep 2015), and merged them into one file (referred to as the "viral reference file") in fasta file format. Merge all virus fasta file into one big fasta file called `viruses.fa` . For this tutorial, we have provided this file through google drive [**here**](https://drive.google.com/drive/folders/0B3-883ME4sP3Wm1FVjdVcEpfek0?usp=sharing).
- We have also indexed the viral reference file, so that these files are ready for alignment tools Bowtie2 (folder name: `virus.bowtie2.refB`) or BWA (folder name: `viral.bwa.ref`) through google drive [**here**](https://drive.google.com/drive/folders/0B3-883ME4sP3Wm1FVjdVcEpfek0?usp=sharing).

- NCBI also allows to download information/annotation about these viruses from their web site. This information has been provided as [**Complete_Sequence_info.csv**](https://docs.google.com/spreadsheets/d/1qN_ZcPDPZnJZXDdutjpTlUt8QY9K4VCQvmHdnHZU_j8/edit?usp=sharing).
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