BOL: Related items

ART: Set of Simulation Tools

Jit — Thu, 03 Nov 2016 08:28:25 -0500

ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for the simulation study of the 1000 Genomes Project . ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format. ART can be used together with genome variants simulators (e.g. VarSim) for evaluating variant calling tools or methods.

Address of the bookmark: http://www.niehs.nih.gov/research/resources/software/biostatistics/art/

R Graphs !!

Jit — Fri, 04 Nov 2016 10:48:00 -0500

The blog is a collection of script examples with example data and output plots. R produce excellent quality graphs for data analysis, science and business presentation, publications and other purposes. Self-help codes and examples are provided. Enjoy nice graphs !!

Address of the bookmark: http://rgraphgallery.blogspot.be/

Software for genome assembly !

LEGE — Sun, 30 Aug 2020 09:51:38 -0500

List of bioinformatics tools/Software Website References for genome assembly:

1 Falcon https://github.com/PacificBiosciences/pb-assembly

2 Canu assembler http://canu.readthedocs.io/en/latest/index.html

3 Miniasm assembler https://github.com/lh3/miniasm

4 PBJelly scaffolding tool https://sourceforge.net/projects/pb-jelly/

5 ARCS scaffolding tool https://github.com/bcgsc/arcs

6 Redundans reduction and scaffolding tool https://github.com/Gabaldonlab/redundans

7 Arrow error correction https://github.com/PacificBiosciences/ GenomicConsensus

8 PILON error correction https://github.com/broadinstitute/pilon/wiki

9 BUSCO single copy gene markers http://busco.ezlab.org/

10 Bandage graph assembly viewer https://rrwick.github.io/Bandage/

11 Gepard dotter http://cube.univie.ac.at/gepard

12 MUMmer aligner and plotter http://mummer.sourceforge.net/

Bioinformatics tools for genome assembly !

BioStar — Mon, 24 Jul 2023 07:04:26 -0500

There are numerous genome assembly tools available, each with its strengths and weaknesses. Here is a list of some widely used genome assembly tools as of my last update in September 2021:

SPAdes: An assembler specifically designed for single-cell and multi-cell bacterial genomes, as well as small eukaryotic genomes.
ABySS: A parallelized assembler for large genomes that uses de Bruijn graphs.
Velvet: Another de Bruijn graph-based assembler optimized for short-read sequencing data.
SOAPdenovo: A de Bruijn graph-based assembler designed for short reads, widely used for assembling large and complex genomes.
MaSuRCA: A hybrid assembler that combines data from multiple sequencing technologies, such as Illumina and PacBio.
Canu: A long-read assembler optimized for PacBio and Oxford Nanopore sequencing data.
Flye: A long-read assembler suitable for bacterial and small eukaryotic genomes.
SMARTdenovo: An assembler designed for long reads, particularly suited for PacBio data.
SPAdes Long Read (SPAdesLR): An extension of SPAdes for long-read data, such as those from PacBio or Nanopore.
Minia: An assembler optimized for low memory consumption, suitable for small and medium-sized genomes.
Unicycler: A hybrid assembler that combines short and long reads for circular bacterial genome assembly.
wtdbg2: A de Bruijn graph assembler for long reads, efficient for very large genomes.
Shasta: A long-read assembler that uses the Overlap-Layout-Consensus approach, suitable for PacBio and Nanopore data.
Sparc: An assembler designed to handle noisy long reads from Nanopore sequencing.
CANA: An assembler for metagenomic data, particularly for complex and diverse microbial communities.
Ra Assembler: A metagenome assembler for long reads, designed for highly complex metagenomic samples.

Please note that the field of bioinformatics is constantly evolving, and new assembly tools may have emerged since my last update. Additionally, the performance of these tools can vary depending on the characteristics of the sequencing data and the genome being assembled. When selecting an assembly tool, consider the specific requirements of your project, the available data types, and the computational resources at your disposal. Always refer to the respective tool's documentation and publications for the most up-to-date information and recommendations.

Scripts

Jit — Wed, 30 Nov 2016 10:35:15 -0600

Useful script for NGS analysis.

Address of the bookmark: http://augustus.gobics.de/binaries/scripts/

e-RGA: enhanced Reference Guided Assembly of Complex Genomes

Jit — Mon, 19 Dec 2016 05:56:14 -0600

Next Generation Sequencing has totally changed genomics: we are able to produce huge amounts of data at an incredibly low cost compared to Sanger sequencing. Despite this, some old problems have become even more difficult, de novo assembly being on top of this list. Despite efforts to design tools able to assemble, de novo, an organism sequenced with short reads, the results are still far from those achievable with long reads. In this paper, we propose a novel method that aims to improve de novo assembly in the presence of a closely related reference. The idea is to combine de novo and reference-guided assembly in order to obtain enhanced results.

Address of the bookmark: http://journal.embnet.org/index.php/embnetjournal/article/view/208

EAGER

Jit — Sat, 10 Dec 2016 18:07:23 -0600

The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process.

EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0918-z

Address of the bookmark: https://github.com/apeltzer/EAGER-GUI

MCscan

Bulbul — Thu, 22 Dec 2016 03:53:58 -0600

MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors. This is the toolset for generating the synteny correspondences in Plant Genome Duplication Database. It is intended as an easy-to-use and quick way to identify conserved gene arrays both within the same genome and across different genomes.

More at http://chibba.agtec.uga.edu/duplication/mcscan/

Address of the bookmark: http://chibba.agtec.uga.edu/duplication/mcscan/

QUAST: quality assessment tool for genome assemblies

Jitendra Prajapati — Wed, 06 Apr 2016 18:23:33 -0500

QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.
It can works both with and without a given reference genome.
The tool accepts multiple assemblies, thus is suitable for comparison.

More at http://bioinf.spbau.ru/quast

http://bioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long

GKNO

Jit — Tue, 17 Jan 2017 03:35:34 -0600

gkno opens the world of complex bioinformatic analysis to people of all level of computational expertise. This site contains documentation, tutorials and information on all the tools that comprise gkno.

More at http://gkno.me/

Address of the bookmark: http://gkno.me/