The NGS technologies have the potential to dramatically accelerate biomedical research by enabling
comprehensive analysis of genomes and transcriptomes to become inexpensive, routine, and
widespread tools. This workshop will focus on methods for base‐calling and variant‐calling, for aligning
reads to reference sequences (e.g. genomes), and for de novo assembly of short reads into longer
sequences. The following tools will be covered on Orchestra, a shared research cluster; quality reports
of FASTQ files, trimming and filtering of reads, alignment and coverage objects such as SAM/BAM files
using bowtie/bwa, calling SNPs with Samtools, and De novo Assembly using Velvet.

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