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Day 1: Linux/TACC Introduction
Day 2: Raw Sequencing data manipulation
- Pre-processing FASTQ sequences
- Overview of NGS data formats and analyses
- The FASTA sequencing data format
- The FASTQ sequencing data format, with Illumina/GSAF-specific details
- Compression, Linux manipulation of fastq files
- Overview of sequence quality checking
- FASTQC - a good place to start
- FASTX toolkit manipulation of FASTQ data
- Adapter trimming with cutadapt
- Batch manipulation of FASTQ files
