Bioinformatics : A practical Guide to Next Generation Sequencing Data Analysis (Paperback)

Sequencing and Raw Sequence Data Quality Control, Nucleic acids, Sequencing, Sequencing depth and read quality, FASTQ files, FASTQ read quality assessment, Preprocessing of the FASTQ reads, Mapping of sequence reads to the reference genomes, Introduction to sequence mapping, Read mapping, Read sequence alignment and aligners, Manipulating alignments in SAM/BAM files, Reference-guided genome assembly, De novo Genome Assembly, Introduction to De Novo genome assembly, Examples of De Novo assemblers, Genome Assembly Quality Assessment, Variant Discovery, Introduction to genetic variations, Variant calling programs, Visualizing variants, Variant annotation and prioritization, RNA-seq data analysis, Introduction to RNA-seq, RNA-seq data applications, RNA-seq data analysis workflow, Chromatin Immunoprecipitation sequencing, Introduction to chromatin immunoprecipitation, ChIP sequencing, ChIP-seq analysis workflow, Targeted Gene Metagenomic Data Analysis, Introduction to metagenomics, Analysis workflow, Data Analysis with QIIME2, Shotgun metagenomic data analysis, Introduction, Shotgun metagenomic analysis workflow