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

🌺 reference-free transcriptome assembly for short and long 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

Learning to untangle genome assembly with graph neural networks.

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.

A simple DSL2 workflow: tutorial

Basic workflow for nanopore sequencing data

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

Germline DNM caller based on LdBG assembly of pathogens

Iterative Organellar Genome Assembly

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

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