<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36867?offset=190 https://bioinformaticsonline.com/bookmarks/view/38012/cosine-non-seeding-method-for-mapping-long-noisy-sequences Fri, 26 Oct 2018 00:41:59 -0500 https://bioinformaticsonline.com/bookmarks/view/38012/cosine-non-seeding-method-for-mapping-long-noisy-sequences <![CDATA[COSINE: non-seeding method for mapping long noisy sequences]]> Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long reads contaminated by a high level of errors.

Address of the bookmark: https://github.com/SUwonglab/COSINE

]]> Jit 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/23167/graphmap-a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads Mon, 06 Jul 2015 08:46:53 -0500 https://bioinformaticsonline.com/bookmarks/view/23167/graphmap-a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads <![CDATA[GraphMap - A highly sensitive and accurate mapper for long, error-prone reads]]> GraphMap is a novel mapper targeted at aligning long, error-prone third-generation sequencing data.
It is designed to handle Oxford Nanopore MinION 1d and 2d reads with very high sensitivity and accuracy, and also presents a significant improvement over the state-of-the-art for PacBio read mappers.

GraphMap was also designed for ease-of-use: the default parameters can handle a wide range of read lengths and error profiles, including: Illumina, PacBio and Oxford Nanopore.
This is an especially important feature for technologies where the error rates and error profiles can vary widely across, or even within, sequencing runs.

http://biorxiv.org/content/early/2015/06/10/020719

Address of the bookmark: https://github.com/isovic/graphmap

]]> Rahul Agarwal 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

]]> biogeek https://bioinformaticsonline.com/bookmarks/view/38762/katuali-is-a-flexible-consensus-pipeline-implemented-in-snakemake-to-basecall-assemble-and-polish-oxford-nanopore-technologies-sequencing-data Tue, 22 Jan 2019 06:26:55 -0600 https://bioinformaticsonline.com/bookmarks/view/38762/katuali-is-a-flexible-consensus-pipeline-implemented-in-snakemake-to-basecall-assemble-and-polish-oxford-nanopore-technologies-sequencing-data <![CDATA[Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data]]>
  • Run a pipeline processing fast5s to a consensus in a single command.
  • Recommended fixed "standard" and "fast" pipelines.
  • Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath.
  • Seemless distribution of tasks over local or distributed compute.
  • Highly configurable.
  • Open source (Mozilla Public License 2.0).

    • Documentation can be found at https://nanoporetech.github.io/katuali/.

    Address of the bookmark: https://github.com/nanoporetech/katuali

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data Thu, 23 Nov 2017 09:55:57 -0600 https://bioinformaticsonline.com/bookmarks/view/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data <![CDATA[poRe: an R package for the visualization and analysis of nanopore sequencing data]]> Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.

    Results: Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.

    Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/ . A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/

    Contact:mick.watson@roslin.ed.ac.uk

    Address of the bookmark: https://academic.oup.com/bioinformatics/article/31/1/114/2365693

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/37524/fmlrc-a-long-read-error-correction-tool-using-the-multi-string-burrows-wheeler-transform Fri, 10 Aug 2018 13:29:28 -0500 https://bioinformaticsonline.com/bookmarks/view/37524/fmlrc-a-long-read-error-correction-tool-using-the-multi-string-burrows-wheeler-transform <![CDATA[FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform]]> FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data. Given a BWT of the short-read sequencing data, FMLRC will build an FM-index and use that as an implicit de Bruijn graph. Each long read is then corrected independently by identifying low frequency k-mers in the long read and replacing them with the closest matching high frequency k-mers in the implicit de Bruijn graph. In contrast to other de Bruijn graph based implementations, FMLRC is not restricted to a particular k-mer size and instead uses a two pass method with both a short "k-mer" and a longer "K-mer". This allows FMLRC to correct through low complexity regions that are computational difficult for short k-mers.

    Address of the bookmark: https://github.com/holtjma/fmlrc

    ]]>     Neel     https://bioinformaticsonline.com/bookmarks/view/35061/proovread-large-scale-high-accuracy-pacbio-correction-through-iterative-short-read-consensus Fri, 05 Jan 2018 04:12:20 -0600 https://bioinformaticsonline.com/bookmarks/view/35061/proovread-large-scale-high-accuracy-pacbio-correction-through-iterative-short-read-consensus <![CDATA[proovread : large-scale high-accuracy PacBio correction through iterative short read consensus]]> proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

    proovread maps high coverage data to pacbio reads (bwa mem, blasr, daligner) in multiple iterations.

    Address of the bookmark: https://github.com/BioInf-Wuerzburg/proovread

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/41148/pbmm2a-minimap2-frontend-for-pacbio-native-data-formats Tue, 18 Feb 2020 03:36:22 -0600 https://bioinformaticsonline.com/bookmarks/view/41148/pbmm2a-minimap2-frontend-for-pacbio-native-data-formats <![CDATA[pbmm2:A minimap2 frontend for PacBio native data formats]]> pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.

    Address of the bookmark: https://github.com/PacificBiosciences/pbmm2

    ]]>     BioStar     https://bioinformaticsonline.com/bookmarks/view/42530/shovill-assemble-bacterial-isolate-genomes-from-illumina-paired-end-reads Sat, 02 Jan 2021 07:05:36 -0600 https://bioinformaticsonline.com/bookmarks/view/42530/shovill-assemble-bacterial-isolate-genomes-from-illumina-paired-end-reads <![CDATA[shovill: Assemble bacterial isolate genomes from Illumina paired-end reads]]> Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.

    Address of the bookmark: https://github.com/tseemann/shovill

    ]]>     BioStar