<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/41673?offset=140 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/44223/ale-assembly-likelihood-estimator Wed, 08 Mar 2023 01:39:33 -0600 https://bioinformaticsonline.com/bookmarks/view/44223/ale-assembly-likelihood-estimator <![CDATA[ALE: Assembly Likelihood Estimator]]> Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly.  Depending on your genome size you may want to convert the .wig files to the BigWig format.

Address of the bookmark: https://github.com/sc932/ALE

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43846/the-complete-sequence-of-a-human-genome Thu, 31 Mar 2022 23:58:18 -0500 https://bioinformaticsonline.com/bookmarks/view/43846/the-complete-sequence-of-a-human-genome <![CDATA[The complete sequence of a human genome]]> The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Address of the bookmark: https://www.science.org/doi/10.1126/science.abj6987

]]> Neel https://bioinformaticsonline.com/bookmarks/view/43909/human-complete-genome Wed, 06 Jul 2022 06:42:55 -0500 https://bioinformaticsonline.com/bookmarks/view/43909/human-complete-genome <![CDATA[Human Complete Genome]]> Telomere-to-telomere consortium

We have sequenced the CHM13hTERT human cell line with a number of technologies. Human genomic DNA was extracted from the cultured cell line. As the DNA is native, modified bases will be preserved. The data includes 30x PacBio HiFi, 120x coverage of Oxford Nanopore, 70x PacBio CLR, 50x 10X Genomics, as well as BioNano DLS and Arima Genomics HiC. Most raw data is available from this site, with the exception of the PacBio data which was generated by the University of Washington/PacBio and is available from NCBI SRA.

A UCSC browser is available for v2.0 (as well as legacy v1.0 and v1.1 versions). An interactive dotplot visualization of all genomic repeats is also available from resgen.io. Known issues identified in the assembly are tracked at CHM13 issues.

 

MORE at https://github.com/marbl/CHM13

Address of the bookmark: https://www.science.org/doi/10.1126/science.abj6987

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/40465/airlift-a-methodology-and-tool-for-comprehensively-moving-mappings-and-annotations-from-one-genome-to-another-similar-genome Mon, 23 Dec 2019 10:20:13 -0600 https://bioinformaticsonline.com/bookmarks/view/40465/airlift-a-methodology-and-tool-for-comprehensively-moving-mappings-and-annotations-from-one-genome-to-another-similar-genome <![CDATA[AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome]]> We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.

Address of the bookmark: https://github.com/CMU-SAFARI/AirLift

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41896/kad-assessing-genome-assemblies-using-k-mer-copies-in-assemblies-and-k-mer-abundance-in-illumina-reads Fri, 19 Jun 2020 07:34:12 -0500 https://bioinformaticsonline.com/bookmarks/view/41896/kad-assessing-genome-assemblies-using-k-mer-copies-in-assemblies-and-k-mer-abundance-in-illumina-reads <![CDATA[KAD: Assessing genome assemblies using K-mer copies in assemblies and K-mer abundance in Illumina reads]]> KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per k-mer, K-mer Abundance Difference (KAD), which indicates how well the assembly matches read data for each k-mer.

image

where, c is the count of a k-mer from reads, m is the mode of counts of read k-mers, and n is the copy of the k-mer in the assembly.

Address of the bookmark: https://github.com/liu3zhenlab/KAD

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