<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/40792?offset=160 https://bioinformaticsonline.com/bookmarks/view/37785/haplomerger2-rebuilding-both-haploid-sub-assemblies-from-high-heterozygosity-diploid-genome-assembly Thu, 27 Sep 2018 07:08:47 -0500 https://bioinformaticsonline.com/bookmarks/view/37785/haplomerger2-rebuilding-both-haploid-sub-assemblies-from-high-heterozygosity-diploid-genome-assembly <![CDATA[HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly]]> HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a hierarchical scaffolding procedure and a reliable gap-closing method for haploid sub-assemblies.

Source code, executables and the testing dataset are freely available at https://github.com/mapleforest/HaploMerger2/releases/.

Address of the bookmark: https://github.com/mapleforest/HaploMerger2/releases/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/38063/referee-genome-assembly-quality-scores Sun, 04 Nov 2018 16:44:30 -0600 https://bioinformaticsonline.com/bookmarks/view/38063/referee-genome-assembly-quality-scores <![CDATA[Referee: Genome assembly quality scores]]> Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site in an assembled genome to calculate a quality score for each position in the genome assembly.

We accomplish this by first calculating genotype likelihoods for every site. For a given site in a diploid genome, there are 10 possible genotypes (AA, AC, AG, AT, CC, CG, CT, GG, GT, TT). Referee takes as input the genotype likelihoods calculated for all 10 genotypes given the called reference base at each position.

Referee is a program to calculate a quality score for every position in a genome assembly. This allows for easy filtering of low quality sites for any downstream analysis.

https://github.com/gwct/referee

Address of the bookmark: https://gwct.github.io/referee/#

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39253/gmass-a-novel-measure-for-genomeassembly-structural-similarity Sun, 14 Apr 2019 20:35:40 -0500 https://bioinformaticsonline.com/bookmarks/view/39253/gmass-a-novel-measure-for-genomeassembly-structural-similarity <![CDATA[GMASS: a novel measure for genomeassembly structural similarity]]>

The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2710-z

Address of the bookmark: http://bioinfo.konkuk.ac.kr/GMASS/htdocs/syncircos.php

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/40946/free-genomics-data Fri, 07 Feb 2020 14:08:31 -0600 https://bioinformaticsonline.com/bookmarks/view/40946/free-genomics-data <![CDATA[Free Genomics data !]]> The specimens were collected by the Oxford Wytham Woods and Edinburgh Lohse lab teams. DNA extraction and sequencing was carried out by the Sanger Institute Scientific Operations teams. Assemblies were carried out by the Tree of Life team (Shane McCarthy) and colleagues in Pacific Biosciences (Jonas Korlach).

https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/

Address of the bookmark: https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/41459/jcvipython-utility-libraries-on-genome-assembly-annotation-and-comparative-genomics Tue, 17 Mar 2020 06:19:06 -0500 https://bioinformaticsonline.com/bookmarks/view/41459/jcvipython-utility-libraries-on-genome-assembly-annotation-and-comparative-genomics <![CDATA[JCVI:Python utility libraries on genome assembly, annotation and comparative genomics]]> Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

https://github.com/tanghaibao/jcvi

More at https://github.com/tanghaibao/jcvi/wiki

Address of the bookmark: https://github.com/tanghaibao/jcvi

]]> Jit https://bioinformaticsonline.com/blog/view/42166/software-for-genome-assembly Sun, 30 Aug 2020 09:51:38 -0500 https://bioinformaticsonline.com/blog/view/42166/software-for-genome-assembly <![CDATA[Software for genome assembly !]]> 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/

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/43614/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-annotation-and-visualization Tue, 30 Nov 2021 23:23:57 -0600 https://bioinformaticsonline.com/bookmarks/view/43614/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-annotation-and-visualization <![CDATA[MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization]]> MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads.

https://academic.oup.com/nar/article/47/11/e63/5377471

Address of the bookmark: https://github.com/linzhi2013/MitoZ

]]> Neel https://bioinformaticsonline.com/pages/view/44352/bioinformatics-tools-for-genome-assembly Mon, 24 Jul 2023 07:04:26 -0500 https://bioinformaticsonline.com/pages/view/44352/bioinformatics-tools-for-genome-assembly <![CDATA[Bioinformatics tools for genome assembly !]]> 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:

  1. SPAdes: An assembler specifically designed for single-cell and multi-cell bacterial genomes, as well as small eukaryotic genomes.

  2. ABySS: A parallelized assembler for large genomes that uses de Bruijn graphs.

  3. Velvet: Another de Bruijn graph-based assembler optimized for short-read sequencing data.

  4. SOAPdenovo: A de Bruijn graph-based assembler designed for short reads, widely used for assembling large and complex genomes.

  5. MaSuRCA: A hybrid assembler that combines data from multiple sequencing technologies, such as Illumina and PacBio.

  6. Canu: A long-read assembler optimized for PacBio and Oxford Nanopore sequencing data.

  7. Flye: A long-read assembler suitable for bacterial and small eukaryotic genomes.

  8. SMARTdenovo: An assembler designed for long reads, particularly suited for PacBio data.

  9. SPAdes Long Read (SPAdesLR): An extension of SPAdes for long-read data, such as those from PacBio or Nanopore.

  10. Minia: An assembler optimized for low memory consumption, suitable for small and medium-sized genomes.

  11. Unicycler: A hybrid assembler that combines short and long reads for circular bacterial genome assembly.

  12. wtdbg2: A de Bruijn graph assembler for long reads, efficient for very large genomes.

  13. Shasta: A long-read assembler that uses the Overlap-Layout-Consensus approach, suitable for PacBio and Nanopore data.

  14. Sparc: An assembler designed to handle noisy long reads from Nanopore sequencing.

  15. CANA: An assembler for metagenomic data, particularly for complex and diverse microbial communities.

  16. 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.

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44549/quartet-a-telomere-to-telomere-toolkit-for-gap-free-genome-assembly-and-centromeric-repeat-identification Sat, 08 Jun 2024 15:54:36 -0500 https://bioinformaticsonline.com/bookmarks/view/44549/quartet-a-telomere-to-telomere-toolkit-for-gap-free-genome-assembly-and-centromeric-repeat-identification <![CDATA[quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification.]]> quarTeT is a collection of tools for T2T genome assembly and basic analysis in automatic workflow.

Task include:

https://academic.oup.com/hr/article/10/8/uhad127/7197191?login=false 

Address of the bookmark: http://www.atcgn.com:8080/quarTeT/home.html

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/26303/maker Sun, 07 Feb 2016 15:59:24 -0600 https://bioinformaticsonline.com/bookmarks/view/26303/maker <![CDATA[MAKER]]> MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.

More at http://www.yandell-lab.org/software/maker.html

Address of the bookmark: http://www.yandell-lab.org/software/maker.html

]]> Jitendra Narayan