Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

Simple bacterial assembly and annotation pipeline

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

De novo assembly based variant calling pipeline for Illumina short reads

Standalone C library for assembling Illumina short reads in small regions

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

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

Learning to untangle genome assembly with graph neural networks.

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

Basic workflow for nanopore sequencing data

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

A simple DSL2 workflow: tutorial

🌺 reference-free transcriptome assembly for short and long reads

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

Iterative Organellar Genome Assembly

Germline DNM caller based on LdBG assembly of pathogens

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

Biocore's de novo transcriptome assembly workflow based on Nextflow