BOL: Related items

Circlator: automated circularization of genome assemblies using long sequencing reads

Poonam Mahapatra — Tue, 15 May 2018 09:42:32 -0500

A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-0849-0. PMID: 26714481.

Address of the bookmark: http://sanger-pathogens.github.io/circlator/

P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

BioStar — Fri, 07 Sep 2018 05:19:06 -0500

P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides another practical alternative to existing mate-pair_based approaches or other Protein-based approaches (for instance, PEP_scaffolder ) for scaffolding genome sequences. The most important feature of this method is to improve the completeness of gene regions and long-coding gene regions (for instance, circRNA).

Address of the bookmark: http://www.fishbrowser.org/software/P_RNA_scaffolder/#

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/

AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references

Manisha Mishra — Tue, 17 Apr 2018 16:21:20 -0500

AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism.

Using AlignGraph

AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome.fa --distanceLow distanceLow --distanceHigh distancehigh --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa [--kMer k --insertVariation insertVariation --coverage coverage --part p --fastMap --ratioCheck --iterativeMap --misassemblyRemoval --resume]

Address of the bookmark: https://github.com/baoe/AlignGraph

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

Understanding PacBio

Jitendra Narayan — Fri, 24 Feb 2017 10:17:36 -0600

This tutorial includes resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts. Below are links to training modules (webinars and PowerPoint presentations) to help you get started with your data processing, as well as information for specialized applications.

Training Resources:

Specialized Applications:

Address of the bookmark: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki

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

GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads

Jit — Mon, 14 May 2018 05:25:48 -0500

This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this documentation, is distributed free of charge. If you use this program in a publication, please cite the following reference:
Chong Chu, Xin Li, and Yufeng Wu. "GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads." bioRxiv (2017): 125534.

Address of the bookmark: https://github.com/Reedwarbler/GAPPadder

De novo Genome Assembly for Illumina Data

Rahul Nayak — Mon, 20 Jan 2020 05:13:29 -0600

Written and maintained by Simon Gladman - Melbourne Bioinformatics (formerly VLSCI)

Protocol Overview / Introduction

In this protocol we discuss and outline the process of de novo assembly for small to medium sized genomes.

https://www.melbournebioinformatics.org.au/tutorials/tutorials/assembly/assembly-protocol/

Address of the bookmark: https://www.melbournebioinformatics.org.au/tutorials/tutorials/assembly/assembly-protocol/

Metassembler: merging and optimizing de novo genome assemblies

Rahul Nayak — Tue, 08 May 2018 04:52:33 -0500

Metassembler combines multiple whole genome de novo assemblies into a combined consensus assembly using the best segments of the individual assemblies.

Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence.

Address of the bookmark: https://sourceforge.net/projects/metassembler/?source=directory