Bioinformatics pipeline configuration

Hi. I can config a pipeline for NGS data processing on your Linux machine.

• NGS data quality control: FastQC;
• Read preparation: cutadapt;
• Read mapping: BWA, Bowtie2, HISAT2;
• GATK: MarkDuplicates, BQSR;
• SAMtools;
• Variant calling;
• Interval manipulation: BEDtools;
• Cohort analysis;
• Variant annotation: ANNOVAR, Ensembl VEP;
• Reference sequence preparation;
• Downloading up-to-date annotation databases.