BOL: Related items

Ra assembler - a de novo DNA assembler for third generation sequencing data

biogeek — Wed, 27 Dec 2017 20:36:54 -0600

Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS).

Ra is in development since 2014 in the form of several separate components that used to be run individually.
This project aims to ease the usage of Ra by integrating it into a complete de novo assembly tool.

Unlike other state-of-the-art assemblers, Ra does not have an error correction step. Instead, it relies on detecting overlaps using a very sensitive and specific overlapper ("graphmap -w owler", https://github.com/isovic/graphmap) and constructing and reducing an overlap graph (Ra layout, https://github.com/mariokostelac/ra).

Address of the bookmark: https://github.com/mariokostelac/ra-integrate/

Cerulean: A hybrid assembly using high throughput short and long reads

Rahul Nayak — Tue, 05 Jun 2018 10:10:15 -0500

Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in Deshpande, V., Fung, E. D., Pham, S., & Bafna, V. (2013). Cerulean: A hybrid assembly using high throughput short and long reads. arXiv preprint arXiv:1307.7933. http://arxiv.org/abs/1307.7933

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

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

Abhi — Tue, 05 Sep 2023 07:31:35 -0500

MitoHiFi v3.2 is a python pipeline distributed under MIT License !

MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project (DToL)

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05385-y

Address of the bookmark: https://github.com/marcelauliano/MitoHiFi

VAGUE:Velvet Assembler Graphical Front End

Jit — Fri, 24 Feb 2017 08:56:49 -0600

VAGUE is a vague acronym for "Velvet Assembler Graphical Front End", which means it is a GUI for the Velvet de novo assembler. The command line version of Velvet can be complicated for beginners to use, but VAGUE makes it clear and simple

More at http://www.vicbioinformatics.com/software.vague.shtml

Address of the bookmark: http://www.vicbioinformatics.com/software.vague.shtml

Minia

Jit — Thu, 08 Dec 2016 05:07:00 -0600

Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).

Download

Minia 2.0.7 Linux 64-bits binaries (Source code) (Legacy codebase)

For the impatient

A typical Minia command line looks like:

./minia -in reads.fa -kmer-size 31 -abundance-min 3 -out output_prefix

Type

./minia

for a quick explanation of the parameters.

For more information, refer to the manual.

KmerGenie can be used to determine the best k-mer size, minimum abundance of correct k-mers, and genome size estimation for your dataset.

Address of the bookmark: http://minia.genouest.org/

GARM:Genome Assembly, Reconciliation and Merging

Jit — Mon, 19 Dec 2016 06:03:02 -0600

The pipeline is based mainly implemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al., 2000) and MUMmer (Kurtz et al., 2004) packages. The pipeline was tested on Debian, Ubuntu, Fedora and BioLinux distributions. The method merges contigs or scaffolds from different assemblers using the same or different sequencing technologies. When scaffolds are provided, a process of finding probable compressions or extensions (CE) problems in the assemblies can be per-formed; contigs are joined back into scaffolds after gap recalculation

Address of the bookmark: http://garm-meta-assem.sourceforge.net/

quickmerge: A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

Jit — Mon, 19 Dec 2016 10:23:36 -0600

quickmerge uses a simple concept to improve contiguity of genome assemblies based on long molecule sequences, often with dramatic outcomes. The program uses information from assemblies made with illumina short reads and PacBio long reads to improve contiguities of an assembly generated with PacBio long reads alone. This is counterintuitive because illumina short reads are not typically considered to cover genomic regions which PacBio long reads cannot. Although we have not evaluated this program for assemblies generated with Oxford nanopore sequences, the program should work with ONP-assemblies too.

Address of the bookmark: https://github.com/mahulchak/quickmerge

MetaBAT: An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities

Jit — Mon, 06 Mar 2017 03:44:34 -0600

MetaBAT, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Here we developed an automated metagenome binning software, called MetaBAT, which integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. Tested on both synthetic and real metagenome datasets, MetaBAT outperforms alternative methods in both accuracy and computational efficiency. Applying MetaBAT to an assembly from 1,704 human gut samples formed 1,634 genome bins (>200kb) in 3 hours, where 621 genome bins are >50% complete with <5% contamination from other species. Further analysis shows that the quality of these genome bins approaches manually curated genomes.

Address of the bookmark: https://bitbucket.org/berkeleylab/metabat

ABACAS

Surabhi Chaudhary — Thu, 16 Feb 2017 12:15:55 -0600

ABACAS is intended to rapidly contiguate (align, order, orientate) , visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. It uses MUMmer to find alignment positions and identify syntenies of assembly contigs against the reference. The output is then processed to generate a pseudomolecule taking overlaping contigs and gaps in to account. MUMmer's alignment generating programs, Nucmer and Promer are used followed by the 'delta-filter' utility function. Users could also run tblastx on contigs that are not used to generate the pseudomolecule.

Address of the bookmark: http://abacas.sourceforge.net/Manual.html#9._Colour_code

Multi-metagenome assembly

Radha Agarkar — Fri, 03 Mar 2017 10:14:18 -0600

This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in:

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Mads Albertsen, Philip Hugenholtz, Adam Skarshewski, Gene W. Tyson, Kåre L. Nielsen and Per .H. Nielsen

Nature Biotechnology 2013, doi: 10.1038/nbt.2579

Address of the bookmark: https://github.com/MadsAlbertsen/multi-metagenome