bcftools singularity container
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Updated
Nov 8, 2018 - Shell
bcftools singularity container
scripts and resources for performing miRNA sequencing analysis using tools like mirPRo and miRDeep2. Explore the code to process reads, map them to the genome, quantify known miRNAs, identify novel miRNAs, and browse the results
One-stop shop for one-click NGS analyses from the command-line
A free and easy-to-use pipeline to analyse data from ancient NCR-mtDNA sequences obtained by amplicon-based NGS methods
Performed a differential gene expression analysis with RNA-seq that compares the expression in human control breast cancer cell lines with lines treated by silencing the NRDE2 gene. A Salmon + tximport + DESeq2 workflow was conducted to pursue this.
Raw code to get polymorphisms from samples analysed by using the PowerSeq® CRM Nested System kit (Promega Corporation)
Complete Pipeline for RNA-seq data analysis: From FastQ to differntial gene expression to annotated Variations.
Parallel / multithreading / multiple threads version of Prinseq
Identification of transposon sites on yeast genome (S. cerevisiae) using DNAseq data.
BIO634 Next-Generation Sequencing 2 – Transcriptomes, Variant Calling and Biological Interpretation
Geno-DeBasher package for detection of germline and somatic variants
Materials & Methods for CNV calling with Genalice software against a benchmark dataset
WGS pipeline
NGS pipeline for somatic variant calling from amplicon datasets
Sentieon DNAscope + Machine Learning Model
eXome Hidden Markov model (XHMM) - Copy Number Variants (CNVs) from Whole Exome Sequencing Data
Utilities for analyzing next generation sequencing data.
Documentation on St. Jude Cloud.
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
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