Ghosh, Priyanka, Sriram Krishnamoorthy, and Ananth Kalyanaraman.
“PaKman: A Scalable Algorithm for Generating Genomic Contigs on Distributed Memory Machines.”
IEEE Transactions on Parallel and Distributed Systems (TPDS) vol. 32, no. 5, pp. 1191-1209, 2021. DOI: 10.1109/TPDS.2020.3043241.
CStone is a de novo assembler for RNA-Seq data that uses de Bruijn like graphs and annotates each contig produced with one of three graph classification levels indicating whether or not it can be guaranteed to be non chimeric.
HyAsP is a tool for the extracting plasmids from WGS assemblies in an automatic way. It combines ideas from both reference-based and depth-based methods to identify plasmids in a greedy algorithm, using information on the occurrences of known plasmid genes and considering characteristics of the contigs such as read depth and GC content.
HipMer is a high-performance application that produces high-quality de novo assemblies for very large-scale genomes.
The MetaHipMer extension is a recent addition to HipMer that is geared to large metagenomes and leverages iterative kmer sizes and a specialized scaffolding algorithm to produce increased contiguity and accuracy in metagenomic assemblies. It is able to reconstruct rRNA elements via a separate algorithm which relies on reference SSU and LSU Hidden Markov Models to help traverse the contig graph around ribosomal RNA regions.
Celera Assembler (wgs-assembler) is scientific software for DNA research. It can reconstruct long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing. The Celera Assembler has enabled discovery in microbial genomes, large eukaryotic genomes, diploid genomes, and genomes from environmental samples. Celera Assembler contributed the first diploid sequence of an individual human, and metagenomics assemblies of the Global Ocean Sampling
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).
AMOS (AModular, Open-Source) consortium is committed to the development of open-source whole genome assembly software. The project acronym (AMOS) represents our primary goal — to produce A Modular, Open-Source whole genome assembler.Open-source so that everyone is welcome to contribute and help build outstanding assembly tools, and modular in nature so that new contributions can be easily inserted into an existing assembly pipeline. This modular design will foster the development of new assembly algorithms and allow the AMOS project to continually grow and improve in hopes of eventually becoming a widely accepted and deployed assembly infrastructure. In this sense, AMOS is both a design philosophy and a software system.