BOL: Related items

CABOG: Celera Assembler with Best Overlap Graph

Abhimanyu Singh — Mon, 15 May 2017 05:04:39 -0500

CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as mammalian. CABOG is an extension of the Celera Assembler software that was originally developed at Celera for the 2001 publication of the first draft human genome sequence. The software was released to the public domain in 2004. Its open source repository on Source Forge is an internet resource for scientists around the world.

CABOG is one of many software programs called genome assemblers. These programs exist to overcome the fundamental limitation of all sequencing machines, namely, that they read out very few DNA letters at a time. These programs reconstruct genomes that are billions of letters long from the hundreds of letters per read that modern sequencers provide. What these programs do is often described as a scaled up version of a family solving a jigsaw puzzle.

The CABOG software was the first to accomplish many scientific goals. It was the first to assemble the genome of a multicellular organism (Drosophila melanogaster, 2000). It was the first to assemble both parental haplotypes of one human genome (J. Craig Venter, 2007). It was the first to assemble environmental sequence from the oceans (Sargasso Sea in 2004 and Global Ocean Sampling in 2007). It was first to combine reads from first-generation Sanger sequencing machines and second-generation pyrosequencing machines (Marine microbes, 2006). Today, CABOG is one of the leading assembly programs for data sets that include paired end data from the Roche 454 line of sequencing machines.

Address of the bookmark: http://www.jcvi.org/cms/research/projects/cabog/overview/

BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly

Jit — Mon, 22 May 2017 05:43:51 -0500

This tool is for users to upgrade their metagenomics assemblies using long reads. This includes fixing mis-assemblies and scaffolding/gap-filling. If you encounter any issues, please contact me at kklam@eecs.berkeley.edu. My name is Ka-Kit Lam.

https://github.com/kakitone/MetaFinisherSC

https://github.com/kakitone/BIGMAC

Address of the bookmark: https://github.com/kakitone/BIGMAC

Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.

Jit — Wed, 20 Dec 2017 18:59:42 -0600

Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes. It is a hybrid k-mer/read-based assembler that capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on commodity clusters in under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures.

https://jgi.doe.gov/data-and-tools/meraculous/

https://arxiv.org/ftp/arxiv/papers/1703/1703.09852.pdf

Address of the bookmark: https://sourceforge.net/projects/meraculous20/

Flye: Fast and accurate de novo assembler for single molecule sequencing reads

Jit — Fri, 04 May 2018 19:16:22 -0500

Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After the initial assembly, Flye performs an extra repeat classification and analysis step to improve the structural accuracy of the resulting sequence. The package also includes a polisher module, which produces the final assembly of high nucleotide-level quality.

Address of the bookmark: https://github.com/fenderglass/Flye

Ranbow: a haplotype assembler for polyploid genomes

Jit — Fri, 01 Jun 2018 07:21:54 -0500

Ranbow is a haplotype assembler for polyploid genomes. It has been developed for the haplotype assembly of the hexaploid sweet potato genome, which is highly heterozygous. Ranbow can also be applied to other polyploid genomes. After a first phasing, Ranbow utilizes the assembled haplotypes to improve the accuracy of variant calling results and to infer the evolutionary history of the organism´s genome. Ranbow has three main modes of function: ranbow hap: for haplotyping ranbow eval: for evaluating of the assemble haplotypes by gold standard (long) reads ranbow phylo: for the phylogenetic analysis

Address of the bookmark: https://www.molgen.mpg.de/ranbow

Phased Human Genome Assembly !

Rahul Nayak — Mon, 08 Oct 2018 09:10:54 -0500

The new publicly available assembly (PacBio HG00733) has the fewest gaps of any human genome assembly, with more than half of the genome contained in gapless sequence at least 27 Mb long. The primary contig assembly is 2.89 Gb long and consists of 865 contigs that were assembled with PacBio data generated with the company’s Sequel® System. Using the FALCON-Unzip assembler, maternal and paternal haplotypes were resolved over more than 80% of the genome. Maternal and paternal haplotype blocks were then further phased using Hi-C technology and the FALCON-Phase methoddeveloped in collaboration with Phase Genomics. The genome was then de novo scaffolded using Phase Genomics’ Proximo Hi-C platform, resulting in the first chromosome-scale diploid assembly of a single individual accomplished with only two technologies. More specific details about the assembly are included on the PacBio blog.

The data are available using NCBI accession IDs: BioProject: (PRJNA483067), assembly: [RBJD00000000] and sequence data (SRP155659).

Additional Resources

Interactive map showcasing global initiatives underway to generate reference-quality human genome assemblies for diverse populations
BioReport Podcast on the value of ethnic-specific reference genomes
Nature Reviews Genetics paper from NHGRI: Prioritizing diversity in human genomics research
Article in The Journal of Precision Medicine: “Minority Report – Ethnic Diversity and the Real Promise for Precision Medicine”
Article in Bio-IT World: “Genomic Data Standards Are a Necessity”
NHGRI Project Award: High Quality Human and Non-Human Primate Genome Assemblies

More details are available on the PacBio website:

Blog post: Data Release: Highest-Quality, Most Contiguous Individual Human Genome Assembly to Date
Blog post: For Reference-Grade Human Genome Assemblies, SMRT Sequencing Yields Optimal Results
Webinar: Assembling High-Quality Human Reference Genomes for Global Populations
FALCON-Phase press release and article preprint
PacBio research focus webpage about Human Population Genetics

Ref: https://stockguru.com/2018/10/08/pacific-biosciences-releases-highest-quality-most-contiguous-individual-human-genome-assembly-to-date/

RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs

BioJoker — Wed, 17 Apr 2019 19:45:22 -0500

Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019.

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
Intact ordering and orienting of contigs.
Chimeric contig correction
GFF lift-over
Structural variant calling with and integrated version of Assemblytics
Confidence scores associated with the grouping, localization, and orientation for each contig.

Address of the bookmark: https://github.com/malonge/RaGOO

Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm

BioStar — Mon, 16 Mar 2020 10:09:26 -0500

Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version at https://arxiv.org/pdf/1902.04341.pdf

More at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa179/5804978?rss=1

Address of the bookmark: https://github.com/CMU-SAFARI/Apollo

MitoFinder

Neel — Tue, 29 Aug 2023 02:13:01 -0500

Allio, R., Schomaker-Bastos, A., Romiguier, J., Prosdocimi, F., Nabholz, B., & Delsuc, F. (2020) Mol Ecol Resour. 20, 892-905. (publication link)

Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.

MitoFinder is also designed to find and annotate mitochondrial sequences in existing genomic assemblies (generated from Hifi/PacBio/Nanopore/Illumina sequencing data...)

MitoFinder is distributed under the license.

Address of the bookmark: https://github.com/RemiAllio/MitoFinder

Peregrine & SHIMMER Genome Assembly Toolkit

Abhi — Thu, 16 Dec 2021 02:50:19 -0600

Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus. It uses Sparse HIereachical MimiMizER (SHIMMER) for fast read-to-read overlaping without quadratic comparisions used in other OLC assemblers.

Address of the bookmark: https://github.com/cschin/Peregrine