<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36755?offset=340 https://bioinformaticsonline.com/bookmarks/view/40389/sequila-cov-a-fast-and-scalable-library-for-depth-of-coverage-calculations Sun, 15 Dec 2019 10:19:35 -0600 https://bioinformaticsonline.com/bookmarks/view/40389/sequila-cov-a-fast-and-scalable-library-for-depth-of-coverage-calculations <![CDATA[SeQuiLa-cov: A fast and scalable library for depth of coverage calculations]]> The Docker image is available at https://hub.docker.com/r/biodatageeks/. Supplementary information on benchmarking procedure as well as test data are publicly accessible at the project documentation site http://biodatageeks.org/sequila/benchmarking/benchmarking.html#depth-of-coverage. An archival copy of the code and supporting data is also available via the GigaScience database GigaDB

• Project name: SeQuiLa-cov

• Project home page: http://biodatageeks.org/sequila/

• Source code repository: https://github.com/ZSI-Bio/bdg-sequila

• Operating system: Platform independent

• Programming language: Scala

• Other requirements: Docker

• License: Apache License 2.0

Address of the bookmark: https://academic.oup.com/gigascience/article/8/8/giz094/5543653

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42645/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite Mon, 18 Jan 2021 10:47:56 -0600 https://bioinformaticsonline.com/bookmarks/view/42645/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite <![CDATA[MMseqs2: ultra fast and sensitive sequence search and clustering suite]]> MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.

Address of the bookmark: https://github.com/soedinglab/MMseqs2

]]> Manisha Mishra https://bioinformaticsonline.com/bookmarks/view/44904/termal-a-fast-and-interactive-terminal-based-viewer-for-multiple-sequence-alignments Mon, 22 Sep 2025 23:51:02 -0500 https://bioinformaticsonline.com/bookmarks/view/44904/termal-a-fast-and-interactive-terminal-based-viewer-for-multiple-sequence-alignments <![CDATA[Termal: a fast and interactive terminal-based viewer for multiple sequence alignments]]> termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC) clusters.

https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbaf208/8257678?login=true

Address of the bookmark: https://github.com/sib-swiss/termal

]]> LEGE 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/35057/ectools-long-read-correction-and-other-correction-tools Fri, 05 Jan 2018 04:02:22 -0600 https://bioinformaticsonline.com/bookmarks/view/35057/ectools-long-read-correction-and-other-correction-tools <![CDATA[ECTOOLS: Long Read Correction and other Correction tools]]> Long Read Correction and other Correction tools

This package is a loose collection of scripts. To run the correction
routine see the section below. Descriptions of the other scripts
are at the bottom of this file.

Contact: gurtowsk@cshl.edu

In short, the correction algorithm takes as input the unitigs from a short read assembly and uses them to correct long read data. More background information for the algorithm can be found:
http://schatzlab.cshl.edu/presentations/2013-06-18.PBUserMeeting.pdf

Address of the bookmark: https://github.com/jgurtowski/ectools

]]> Jit https://bioinformaticsonline.com/poll/view/23590/will-minion-nanopore-sequencing-increase-the-number-of-next-generation-sequencing-projects Tue, 04 Aug 2015 05:14:07 -0500 https://bioinformaticsonline.com/poll/view/23590/will-minion-nanopore-sequencing-increase-the-number-of-next-generation-sequencing-projects <![CDATA[Will MinION Nanopore sequencing increase the number of Next Generation Sequencing projects?]]> Will MinION Nanopore sequencing increase the number of Next Generation Sequencing projects?

]]> Strand 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/34704/nanosim-nanopore-sequence-read-simulator-based-on-statistical-characterization Mon, 18 Dec 2017 04:16:31 -0600 https://bioinformaticsonline.com/bookmarks/view/34704/nanosim-nanopore-sequence-read-simulator-based-on-statistical-characterization <![CDATA[NanoSim: nanopore sequence read simulator based on statistical characterization.]]> NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides a comprehensive alignment-based analysis and generates a set of read profiles serving as the input to the next step, the simulation stage. The simulation stage uses the model built in the previous step to produce in silico reads for a given reference genome. NanoSim is written in Python and R. The source files and manual are available at the Genome Sciences Centre website: http://www.bcgsc.ca/platform/bioinfo/software/nanosim

https://github.com/bcgsc/NanoSim

Address of the bookmark: http://www.bcgsc.ca/platform/bioinfo/software/nanosim

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37527/nanopack-visualizing-and-processing-long-read-sequencing-data Fri, 10 Aug 2018 18:41:34 -0500 https://bioinformaticsonline.com/bookmarks/view/37527/nanopack-visualizing-and-processing-long-read-sequencing-data <![CDATA[NanoPack: visualizing and processing long-read sequencing data]]> The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.

 https://academic.oup.com/bioinformatics/article/34/15/2666/4934939

Address of the bookmark: https://github.com/wdecoster/nanoQC

]]> Jit 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

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