NGS Pendrive: a platform-independent customized high-throughput data analysis device
NGS Pendrive: a platform-independent customized high-throughput data analysis device
[version 1; not peer reviewed]No competing interests were disclosed
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★ NGS Basics and Quality Control ★Sequencing Platforms/ Instruments, Basic NGS terminologies, Quality visualization: “Good” and “Bad” reads, Fixed length trimming, Quality based trimming, Adapter clipping and Sequence Duplication removal.
★ Short Read Alignment ★Alignment using BWA, Alignment using BOWTIE, Comparing Aligners, Manipulating SAM output and IGV visualization, the SAM format, filtering and analyzing SAM files, Overview of SAM flags.
★ ChIP seq ★Alignment; finding enriched areas using MACS14, “Glyph” viewing using Ensembl genome browser, Annotating peaks to interpret biological function, Peak decomposition using GEM, DNA motif analysis. Pathway enrichment analysis and Differential Peak Expression, Heatmap and Meta-profile plot with ChiP-seq data, harnessing Public-domain data: ENCODE/UCSC/ Cistrome/GEO,ENA.
★ RNA seq ★Spliced alignment using Tophat2, Transcriptome assembly and Isoform expression, Differential gene Expression using edgeR-DESeq-DESeq2, Visualization of Cuffdiff expression analysis, RNAseq with Kallisto-Salmon. Using HISAT2 and featureCounts.
★ deNovo genome Assembly ★Download and Compile Velvet, Assemble Single-End (SE) and Paired-End (PE) reads, Hybrid-assembly of SE+PE reads, Concepts of Assembling and Scaffolding Contigs to finish the Genome, Assembling using MINIA/ SPADES followed by QUAST-based Icarus Browser Visualization of the Genome Assembly, N50 Statistics.
★ SNP calling ★SAM-representation of variants, OMIM Lookup, Alignment Pileups and VCF format, Annotation and filtering of VCF files using ANNOVAR- Examples, Variant calling on sample data, Multi-sample Variant calling, Variant Normalization and Variant Effect prediction using VEP./ SnpEff.
★ Metagenomics ★Reducing sequencing and PCR errors, Processing improved sequences, Assessing error rates, Processing OTUs, Calling OTUs, Phylotypes, Phylogenetic Analysis, Diversity, Alpha diversity, Beta diversity measurements, Population-level analysis, Phylotype-based analysis, Phylogeny-based analysis
★ NGS Basics and Quality Control ★Sequencing Platforms/ Instruments, Basic NGS terminologies, Quality visualization: “Good” and “Bad” reads, Fixed length trimming, Quality based trimming, Adapter clipping and Sequence Duplication removal.
★ Short Read Alignment ★Alignment using BWA, Alignment... READ MORE
★ NGS Basics and Quality Control ★Sequencing Platforms/ Instruments, Basic NGS terminologies, Quality visualization: “Good” and “Bad” reads, Fixed length trimming, Quality based trimming, Adapter clipping and Sequence Duplication removal.
★ Short Read Alignment ★Alignment using BWA, Alignment using BOWTIE, Comparing Aligners, Manipulating SAM output and IGV visualization, the SAM format, filtering and analyzing SAM files, Overview of SAM flags.
★ ChIP seq ★Alignment; finding enriched areas using MACS14, “Glyph” viewing using Ensembl genome browser, Annotating peaks to interpret biological function, Peak decomposition using GEM, DNA motif analysis. Pathway enrichment analysis and Differential Peak Expression, Heatmap and Meta-profile plot with ChiP-seq data, harnessing Public-domain data: ENCODE/UCSC/ Cistrome/GEO,ENA.
★ RNA seq ★Spliced alignment using Tophat2, Transcriptome assembly and Isoform expression, Differential gene Expression using edgeR-DESeq-DESeq2, Visualization of Cuffdiff expression analysis, RNAseq with Kallisto-Salmon. Using HISAT2 and featureCounts.
★ deNovo genome Assembly ★Download and Compile Velvet, Assemble Single-End (SE) and Paired-End (PE) reads, Hybrid-assembly of SE+PE reads, Concepts of Assembling and Scaffolding Contigs to finish the Genome, Assembling using MINIA/ SPADES followed by QUAST-based Icarus Browser Visualization of the Genome Assembly, N50 Statistics.
★ SNP calling ★SAM-representation of variants, OMIM Lookup, Alignment Pileups and VCF format, Annotation and filtering of VCF files using ANNOVAR- Examples, Variant calling on sample data, Multi-sample Variant calling, Variant Normalization and Variant Effect prediction using VEP./ SnpEff.
★ Metagenomics ★Reducing sequencing and PCR errors, Processing improved sequences, Assessing error rates, Processing OTUs, Calling OTUs, Phylotypes, Phylogenetic Analysis, Diversity, Alpha diversity, Beta diversity measurements, Population-level analysis, Phylotype-based analysis, Phylogeny-based analysis
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