Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
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Updated
Jan 17, 2024 - Shell
Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
Quality Control, Mapping and Reads Count for RNA-Seq Analysis
RNA-seq code with Bowtie alignment and generating strain-specific counts using Emase
Walks through installation and usage of FASTQC, MultiQC, Trimmomatic, and Salmon for transcriptomic data preprocessing. Includes Grid Engine shell scripts that can be looped over many files in a directory.
Back Up of Trimmomatic for learning and testing/modification. Find Original Code at: https://github.com/usadellab/Trimmomatic
Whole Exome Sequencing end-to-end pipeline. Starting from whole exome fastq files: Data QC, Adapter Trimming, Reference Genome Alignment, SAM/BAM Validation, Data Recalibration and Variant Calling.
The repository contain directories of projects done during the bioinformatics degree program
Bulk Rna-seq Analysis
A 10x faster version base on official trimmomatic. The results of trimmomatic-pigz are exactly the same with official trimmomatic.
A comprehensive workflow for de novo assembly of whole-genome shotgun sequencing data using Velvet, followed by BLAST searches to analyze assembled contigs.
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