This is a compilation of my scripts for denovo-RNA-Seq assembly, annotation, and get count metrics for Differential gene expression analysis in Nesi hpc.
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Updated
Jun 22, 2022
This is a compilation of my scripts for denovo-RNA-Seq assembly, annotation, and get count metrics for Differential gene expression analysis in Nesi hpc.
QReadSelector is a subset selection of high-depth next generation sequencing reads for de novo genome assembly using MapReduce framework.
Bioinformatics Pipeline for dRADseq Data
NextFlow pipeline for Virus Variant calling and de novo Assembly of Nanopore and Illumina Reads
CloudEC is a MapReduce-based algorithm for correcting errors in next-generation sequencing big data.
A containerized nextflow pipeline designed to annotate prokaryote genomes.
Inversion status and de novo assembly of Drosophila melanogaster
Identification of transposon insertion sites
Calling SNPs using UNEAK (de novo) pipeline for ponderosa pine
A comprehensive workflow for de novo assembly of whole-genome shotgun sequencing data using Velvet, followed by BLAST searches to analyze assembled contigs.
String Graph Construction on Spark
De novo assembly pipeline for 10X linked-reads, used at the SciLifeLab National Genomics Infrastructure.
Basic workflow for nanopore sequencing data
Python based implementation of De-Novo transcriptome assembly
Workflow Template
Biocore's de novo transcriptome assembly workflow based on Nextflow
Iterative Organellar Genome Assembly
Germline DNM caller based on LdBG assembly of pathogens
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