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

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

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

A simple DSL2 workflow: tutorial

Basic workflow for nanopore sequencing data

Germline DNM caller based on LdBG assembly of pathogens

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

Iterative Organellar Genome Assembly

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

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