A WGS de novo assembler based on the FMD-index for large genomes

QReadSelector is a subset selection of high-depth next generation sequencing reads for de novo genome assembly using MapReduce framework.

Trinity RNA-Seq de novo transcriptome assembly

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

Bioinformatics Pipeline for dRADseq Data

String Graph Construction on Spark

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

Python based implementation of De-Novo transcriptome assembly

Calling SNPs using UNEAK (de novo) pipeline for ponderosa pine

Germline DNM caller based on LdBG assembly of pathogens

Iterative Organellar Genome Assembly

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

De novo assembly based variant calling pipeline for Illumina short reads

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

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

A containerized nextflow pipeline designed to annotate prokaryote genomes.

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.

Standalone C library for assembling Illumina short reads in small regions