denovo-assembly

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

💾 📃 "Reads to report" for public health and clinical microbiology

De novo assembly based variant calling pipeline for Illumina short reads

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

Standalone C library for assembling Illumina short reads in small regions

🌺 reference-free transcriptome assembly for short and long reads

Learning to untangle genome assembly with graph neural networks.

A simple DSL2 workflow: tutorial

Simple bacterial assembly and annotation pipeline

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

Pipeline for de novo peptide sequencing (Novor, DeepNovo, SMSNet, PointNovo, Casanovo) and assembly with ALPS.

Germline DNM caller based on LdBG assembly of pathogens

Iterative Organellar Genome Assembly

UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads

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

String Graph Construction on Spark

Basic workflow for nanopore sequencing data