<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37737?offset=130 https://bioinformaticsonline.com/bookmarks/view/37414/arc-pipeline-which-facilitates-iterative-reference-guided-de-novo-assemblies Thu, 26 Jul 2018 09:20:26 -0500 https://bioinformaticsonline.com/bookmarks/view/37414/arc-pipeline-which-facilitates-iterative-reference-guided-de-novo-assemblies <![CDATA[ARC: pipeline which facilitates iterative, reference guided de novo assemblies]]> ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of:

  1. Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together.
  2. Reducing/removing reference bias as compared to mapping based approaches.

The software is designed to work in situations where a whole-genome assembly is not the objective, but rather when the researcher wishes to assemble discreet 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the traditionally difficult problem of assembly by breaking the reads into small, manageable subsets which can then be assembled quickly and efficiently in parallel. Applications include those in which the researcher wishes to de novo assemble specific content and a set of semi-similar reference targets is available to initialize the assembly process.

https://ibest.github.io/ARC/

Address of the bookmark: https://ibest.github.io/ARC/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38224/novograph-building-whole-genome-graphs-from-long-read-based-de-novo-assemblies Thu, 15 Nov 2018 12:48:30 -0600 https://bioinformaticsonline.com/bookmarks/view/38224/novograph-building-whole-genome-graphs-from-long-read-based-de-novo-assemblies <![CDATA[NovoGraph: building whole genome graphs from long-read-based de novo assemblies]]> NovoGraph: building whole genome graphs from long-read-based de novo assemblies

An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of principle by creating a genome graph of seven ethnically-diverse human genomes.

 

https://f1000research.com/articles/7-1391/v1

Address of the bookmark: https://github.com/NCBI-Hackathons/NovoGraph

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39903/integrative-meta-assembly-pipeline-imap-chromosome-level-genome-assembler-combining-multiple-de-novo-assemblies Sat, 31 Aug 2019 11:30:41 -0500 https://bioinformaticsonline.com/bookmarks/view/39903/integrative-meta-assembly-pipeline-imap-chromosome-level-genome-assembler-combining-multiple-de-novo-assemblies <![CDATA[Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies]]> Chromosome-level genome assembler combining multiple de novo assemblies

https://github.com/jkimlab/IMAP

Address of the bookmark: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0221858

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41920/liftoff-an-accurate-tool-that-maps-annotations-in-gff-or-gtf-between-assemblies Tue, 30 Jun 2020 21:40:52 -0500 https://bioinformaticsonline.com/bookmarks/view/41920/liftoff-an-accurate-tool-that-maps-annotations-in-gff-or-gtf-between-assemblies <![CDATA[Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies]]>  Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a standalone tool that takes two genome assemblies and a reference annotation as input and outputs an annotation of the target genome. 

Address of the bookmark: https://github.com/agshumate/Liftoff

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43867/genomeqc-a-quality-assessment-tool-for-genome-assemblies-and-gene-structure-annotations Thu, 19 May 2022 04:29:05 -0500 https://bioinformaticsonline.com/bookmarks/view/43867/genomeqc-a-quality-assessment-tool-for-genome-assemblies-and-gene-structure-annotations <![CDATA[GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations]]> The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6568-2

Address of the bookmark: https://github.com/HuffordLab/GenomeQC

]]> Neel https://bioinformaticsonline.com/bookmarks/view/37473/lsc-a-long-read-error-correction-tool Thu, 02 Aug 2018 07:39:46 -0500 https://bioinformaticsonline.com/bookmarks/view/37473/lsc-a-long-read-error-correction-tool <![CDATA[LSC :a long read error correction tool]]> Getting Started

These simple steps will help you integrate LSC into your transcriptomics analysis pipeline.

  • Read the LSC_requirements for running LSC.
  • Download and set-up the LSC package.
  • Follow the tutorial to see how LSC works on some example data.
  • Read the manual if anything is unclear.
  • You're ready, Happy LSCing!

Latest publication

Kin Fai Au, Jason Underwood, Lawrence Lee and Wing Hung Wong 
Improving PacBio Long Read Accuracy by Short Read Alignment [Manuscript] 
PLoS ONE 2012. 7(10): e46679. doi:10.1371/journal.pone.0046679

Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/LSC/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43384/lncpipea-nextflow-based-pipeline-for-comprehensive-analyses-of-long-non-coding-rnas-from-rna-seq-datasets Fri, 17 Sep 2021 01:57:02 -0500 https://bioinformaticsonline.com/bookmarks/view/43384/lncpipea-nextflow-based-pipeline-for-comprehensive-analyses-of-long-non-coding-rnas-from-rna-seq-datasets <![CDATA[LncPipe:A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets]]> The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed lncRNAs annotation strategy, optimized calculating efficiency, diversified classification and interactive analysis report. LncPipe allows users additional control in interuppting the pipeline, resetting parameters from command line, modifying main script directly and resume analysis from previous checkpoint.

Ref https://www.lncrnablog.com/lncpipe-a-nextflow-based-pipeline-for-identification-and-analysis-of-long-non-coding-rnas-from-rna-seq-data/

image

Address of the bookmark: https://github.com/likelet/LncPipe

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/34394/tulip-the-uncorrected-long-read-itegration-pipeline Thu, 23 Nov 2017 09:30:01 -0600 https://bioinformaticsonline.com/bookmarks/view/34394/tulip-the-uncorrected-long-read-itegration-pipeline <![CDATA[TULIP - The Uncorrected Long read Itegration Pipeline]]> #Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel)

TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional components and/or implementations are likely to follow. 
Tulipseed takes as input alignments files of long reads to sparse short seeds, and outputs a graph and scaffold structures. Tulipbulb adds long read sequencing data to these.

 

https://github.com/Generade-nl/TULIP

Address of the bookmark: https://github.com/Generade-nl/TULIP

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36632/tulip-the-uncorrected-long-read-integration-pipeline Tue, 15 May 2018 09:06:37 -0500 https://bioinformaticsonline.com/bookmarks/view/36632/tulip-the-uncorrected-long-read-integration-pipeline <![CDATA[TULIP - The Uncorrected Long read Integration Pipeline]]> Address of the bookmark: https://github.com/Generade-nl/TULIP

]]> Jit https://bioinformaticsonline.com/blog/view/34916/bioinformatics-tools-developed-for-oxford-nanopore-data-analysis Wed, 27 Dec 2017 20:47:30 -0600 https://bioinformaticsonline.com/blog/view/34916/bioinformatics-tools-developed-for-oxford-nanopore-data-analysis <![CDATA[Bioinformatics tools developed for Oxford Nanopore data analysis !]]> MinION is the only portable real-time device for DNA and RNA sequencing. Each consumable flow cell can now generate 10–20 Gb of DNA sequence data. Ultra-long read lengths are possible (hundreds of kb) as you can choose your fragment length. One of the technical advantages of ONT data is the read length, which offers great prospects for genome assembly. Generally, assemblers are based on several different types of algorithms, such as greedy, overlap-layout-consensus (OLC), de Bruijn graph (DBG), and string graph.

List of analysis tools developed for Oxford Nanopore data

BWA
Fast nanopore data tuned alignment tool
https://github.com/lh3/bwa

GraphMap
Mapper for long and error-prone reads
https://github.com/isovic/graphmap

LAST
Nanopore tuned alignment tool
http://last.cbrc.jp/

LINKS
Software tool for long read scaffolding
https://github.com/warrenlr/LINKS/

marginAlign
Tools to align nanopore reads to a reference
https://github.com/benedictpaten/marginAlign

minoTour
Real time analysis tools
http://minotour.nottingham.ac.uk/

nanoCORR
Error-correction tool for nanopore sequence data
https://github.com/jgurtowski/nanocorr

NanoOK
Software for nanopore data, quality and error profiles
https://documentation.tgac.ac.uk/display/NANOOK/NanoOK

Nanopolish
Nanopore analysis and genome assembly software
https://github.com/jts/nanopolish

nanopore
Variant-detection tool for nanopore sequence data
https://github.com/mitenjain/nanopore

Nanocorrect
Error-correction tool for nanopore sequence data
https://github.com/jts/nanocorrect/

npReader
Real-time conversion and analysis of nanopore reads
https://github.com/mdcao/npReader

poRe
Tool for analyzing and visualizing nanopore data
https://sourceforge.net/p/rpore/wiki/Home/

PoreSeq
Error-correction and variant-calling software
https://github.com/tszalay/poreseq

Poretools
Nanopore sequence analysis and visualization software
https://github.com/arq5x/poretools

SSPACE-LongRead
Genome scaffolding tool
http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread

SMIS
Genome scaffolding tool
https://sourceforge.net/projects/phusion2/files/smis/

 

List of assemblers for Oxford Nanopore MinION long reads

LQS
DALIGNER, Celera OLC Nanocorrect,
Nanopolish corrector
https://github.com/jts/nanopolish

PBcR
HGAP or BLASR, Celera OLC
PBcR corrector
http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR
–
Canu
MHAP, Celera OLC
Canu corrector
https://github.com/marbl/canu

Falcon
String graph, Celera OLC
Falcon corrector
https://github.com/PacificBiosciences/falcon

Miniasm
OLC
https://github.com/lh3/miniasm

ra-integrate
OLC
https://github.com/mariokostelac/ra-integrate/

ALLPATHS-LG
de Bruijn graph
ALLPATHS-L corrector
https://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12

SPAdes
de Bruijn graph
SPAdes corrector
http://bioinf.spbau.ru/spades

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