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Make Figure 1 visible on Firefox and Chrome #8

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Make Figure 1 visible on Firefox and Chrome #8

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c477acb
Update the path to Figure 1
FlorentCLMichel Feb 1, 2022
7016c6a
Change the alt text of the logo and of Figure 1
FlorentCLMichel Feb 1, 2022
5a3377e
Add a .jpg version of Figure 1
FlorentCLMichel Feb 1, 2022
cac8def
Update README.md
FlorentCLMichel Feb 1, 2022
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4 changes: 2 additions & 2 deletions README.md
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![alt text](https://github.com/KHP-Informatics/DNAscan/blob/master/DNAscan_logo.001.jpeg)
![logo](https://github.com/KHP-Informatics/DNAscan/blob/master/DNAscan_logo.001.jpeg)

# DNAscan
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DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage. DNAscan can analyse 40x whole genome NGS data in ~8 hours, using as little as 8 cpus and 16 Gbs of RAM while guaranteeing a very high performance. We do this by exploiting state-of-the-art bioinformatics tools. DNAscan can screen your DNA NGS data for single nucleotide variants, small indels, structural variants, repeat expansions, viral (or any other organism’s) genetic material. Its results are annotated using a wide range of databases including ClinVar, EXAC, dbSNP and CADD and uploaded onto the gene.iobio platform for an on-the-fly analysis/interpretation.

![alt text](https://github.com/KHP-Informatics/DNAscan/raw/master/DNAscan_pipeline_pic.jp2)
![Figure 1](./DNAscan_pipeline_pic.jpg)

Figure 1. Central panel: Pipeline overview. DNAscan accepts sequencing data, and optionally variant files. The pipeline firstly performs an alignment step (details in the left panel), followed by a customizable data analysis protocol (details in the right panel). Finally, results are annotated and a user friendly report is generated. Right panel: detailed description of the post alignment analysis pipeline (intensive mode). Aligned reads are used by the variant calling pipeline (Freebayes + GATK HC + Bcftools), both aligned and unaligned reads are used by Manta and ExpensionHunter (for which known repeat description files have to be provided) to look for structural variants. The unaligned reads are mapped to a database of known viral genomes (NCBI database) to screen for the presence of their genetic material in the input sequencing data. Left panel: Alignment stage description. Raw reads are aligned with HISAT2. Resulting soft/hard-clipped reads and unaligned reads are realigned with BWA mem and then merged with the others using samtools.

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