Bioinformatics Pipeline for dRADseq Data

Trinity RNA-Seq de novo transcriptome assembly

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.

This project plots the effect of selecting different kmer length parameter in 2 different de novo genome assembly tools - AbySS and Velvet.

A containerized nextflow pipeline designed to annotate prokaryote genomes.

Inversion status and de novo assembly of Drosophila melanogaster

🛠️🧬De Bruijn graph-based genome assembler📈📊

Python based implementation of De-Novo transcriptome assembly

A comprehensive workflow for de novo assembly of whole-genome shotgun sequencing data using Velvet, followed by BLAST searches to analyze assembled contigs.

[A.A. 23/24] R. Napoli

CloudEC is a MapReduce-based algorithm for correcting errors in next-generation sequencing big data.

Identification of transposon insertion sites

Workflow Template

De novo assembly pipeline for 10X linked-reads, used at the SciLifeLab National Genomics Infrastructure.

NextFlow pipeline for Virus Variant calling and de novo Assembly of Nanopore and Illumina Reads

A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq

De novo assembly pipeline for 10X linked-reads using Supernova

String Graph Construction on Spark

Biocore's de novo transcriptome assembly workflow based on Nextflow