<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/39253?offset=90 https://bioinformaticsonline.com/bookmarks/view/32485/bacterial-genome-assembly Fri, 05 May 2017 06:11:22 -0500 https://bioinformaticsonline.com/bookmarks/view/32485/bacterial-genome-assembly <![CDATA[Bacterial genome assembly !!]]> This tutorial will serve as an example of how to use free and open-source genome assembly and secondary scaffolding tools to generate high quality assemblies of bacterial sequence data. The bacterial sample used in this tutorial will be referred to simply as “Species” since it is live data. This data is paired-end data, meaning that there are forward and reverse reads, which we will designate as Sample_R1.fastq and Sample_R2.fastq, respectively.

https://github.com/jennomics/WorkflowPaper/blob/master/Genome%20Assembly%20and%20Annotation.md

Address of the bookmark: http://bioinformatics.uconn.edu/bacterial-genome-assembly-tutorial/

]]> Jit https://bioinformaticsonline.com/news/view/32719/download-assemblies-from-ncbi Mon, 15 May 2017 06:02:32 -0500 https://bioinformaticsonline.com/news/view/32719/download-assemblies-from-ncbi <![CDATA[Download assemblies from NCBI]]> A new “Download assemblies” button is now available in the Assembly database. This makes it easy to download data for multiple genomes without having to write scripts.

For example, you can run a search in Assembly and use check boxes (see left side of screenshot below) to refine the set of genome assemblies of interest. Then, just open the “Download assemblies” menu, choose the source database (GenBank or RefSeq), choose the file type, and start the download. An archive file will be saved to your computer that can be expanded into a folder containing your selected genome data files.

image

 

More at https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/08/genome-data-download-made-easy/

]]> Bulbul https://bioinformaticsonline.com/bookmarks/view/34925/rectangle-graph-for-repeat-resolution-in-genome-assembly Thu, 28 Dec 2017 09:43:03 -0600 https://bioinformaticsonline.com/bookmarks/view/34925/rectangle-graph-for-repeat-resolution-in-genome-assembly <![CDATA[Rectangle Graph for Repeat Resolution in Genome Assembly]]> Ultimate tool for resolving repeats in genome assemblies.

Though the specific implementation of the idea of the rectangle graph approach is already included into the current SPAdes distribution, we're also releasing the Rectangle Graph Module (RGM) as the separate code which can be run independently of SPAdes. Although RGM differs from the current implementation of the rectangle graph approach in SPAdes, in the future we plan to integrate RGM in SPAdes. RGM can be run with other genome assemblers if they use the graph format as SPAdes files.

For more details see: Nikolay Vyahhi, Son K. Pham, Pavel Pevzner. From de Bruijn Graphs to Rectangle Graphs for Genome Assembly, Lecture Notes in Bioinformatics 7534 (2012), pp. 249-261.

Address of the bookmark: http://bioinf.spbau.ru/en/rectangles

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/36478/the-marvel-assembler Fri, 04 May 2018 19:18:41 -0500 https://bioinformaticsonline.com/bookmarks/view/36478/the-marvel-assembler <![CDATA[The MARVEL assembler]]> MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.

The assembly process can be summarized as follows:

  1. overlap
  2. patch reads
  3. overlap (again)
  4. scrubbing
  5. assembly graph construction and touring
  6. optional read correction
  7. fasta file creation

Address of the bookmark: https://github.com/schloi/MARVEL

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37984/baum-%E2%80%93-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus Wed, 24 Oct 2018 23:35:09 -0500 https://bioinformaticsonline.com/bookmarks/view/37984/baum-%E2%80%93-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus <![CDATA[BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus]]> BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the results of existing assemblies that are obtained based on short or long sequencing reads. 

Address of the bookmark: http://www.zhanyuwang.xin/wordpress/index.php/2017/07/21/baum-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40208/ragoo-fast-reference-guided-scaffolding-of-genome-assembly-contigs Sun, 27 Oct 2019 00:57:23 -0500 https://bioinformaticsonline.com/bookmarks/view/40208/ragoo-fast-reference-guided-scaffolding-of-genome-assembly-contigs <![CDATA[RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs]]> 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:

  1. 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.
  2. Intact ordering and orienting of contigs.
  3. Misassembly correction
  4. GFF lift-over
  5. Structural variant calling with and integrated version of Assemblytics
  6. Confidence scores associated with the grouping, localization, and orientation for each contig.

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

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly Mon, 18 May 2020 16:47:56 -0500 https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly <![CDATA[Genobuntu: Package for Next Generation Sequencing and Genome Assembly]]>

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

Features

  • Velvet
  • MiB
  • SSAKE
  • EULER
  • VCAKE
  • ABySS
  • ALLPATHS
  • Celera
  • SHARCGS
  • Allpaths
  • IDBA
  • TAIPAN
  • Edena
  • SOAPdenovo
  • Maq
  • IDBA-UD
  • No. of Reads present in the Ref. Seq.
  • ART NGS Reads Simulator
  • HiTEC, FASTQC
  • Minimum Description Length
  • SOAPaligner
  • Sequencing Read Archive Toolkit

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

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43110/quasimodo-quasispecies-metric-determination-on-omics Sat, 26 Jun 2021 15:22:56 -0500 https://bioinformaticsonline.com/bookmarks/view/43110/quasimodo-quasispecies-metric-determination-on-omics <![CDATA[QuasiModo - Quasispecies Metric Determination on Omics]]> This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In this study we evaluated genome assemblers and variant callers on 10 in vitro generated, mixed strain HCMV sequence samples, each consisting of two lab strains in different abundance ratios. This tool can also be used to evaluate assemblies and variant calling results on other similar datasets.

https://academic.oup.com/bib/article/22/3/bbaa123/5868070

Address of the bookmark: https://github.com/hzi-bifo/Quasimodo

]]> Neel https://bioinformaticsonline.com/bookmarks/view/44489/proksee Wed, 27 Mar 2024 11:11:54 -0500 https://bioinformaticsonline.com/bookmarks/view/44489/proksee <![CDATA[Proksee]]> Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file.

Please Cite the Following
Grant JR, Enns E, Marinier E, Mandal A, Herman EK, Chen C, Graham M, Van Domselaar G, and Stothard P
Nucleic Acids Research, 2023, gkad326, https://doi.org/10.1093/nar/gkad326

Address of the bookmark: https://proksee.ca/

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/43711/vcf-compare Wed, 19 Jan 2022 10:30:14 -0600 https://bioinformaticsonline.com/bookmarks/view/43711/vcf-compare <![CDATA[VCF Compare !]]> compare two BWA mapping methods with the online hg18-mapped data

We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep sequencing platform <ftp://webdata:webdata@ussd-ftp.illumina.com/Data/SequencingRuns/NA18507_GAIIx_100_chr21.bam>, aligned to the b36/hg18 reference genome)

Address of the bookmark: https://wiki.bits.vib.be/index.php/NGS_Exercise.6#compare_aln_.26_mem_results_with_vcf-compare

]]> Rahul Nayak