<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37645?offset=30 https://bioinformaticsonline.com/bookmarks/view/38310/sisrs-site-identification-from-short-read-sequences Wed, 28 Nov 2018 08:56:03 -0600 https://bioinformaticsonline.com/bookmarks/view/38310/sisrs-site-identification-from-short-read-sequences <![CDATA[SISRS: Site Identification from Short Read Sequences]]> Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads must have a fastq file extension.

Address of the bookmark: https://github.com/rachelss/SISRS

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/37643/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads Thu, 06 Sep 2018 16:21:01 -0500 https://bioinformaticsonline.com/bookmarks/view/37643/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads <![CDATA[LoRMA: A tool for correcting sequencing errors in long reads]]> An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are further polished using long-distance dependencies that are found using multiple alignments. According to our experiments, the proposed method is the most accurate one relying on long reads only for read sets with high coverage. Furthermore, when the coverage of the read set is at least 75×, the throughput of the new method is at least 20% higher.

conda install -c atgc-montpellier lorma

Address of the bookmark: https://gite.lirmm.fr/lorma/lorma-releases/wikis/home

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/32190/dbg2olcefficient-assembly-of-large-genomes-using-long-erroneous-reads-of-the-third-generation-sequencing-technologies Wed, 19 Apr 2017 10:09:51 -0500 https://bioinformaticsonline.com/bookmarks/view/32190/dbg2olcefficient-assembly-of-large-genomes-using-long-erroneous-reads-of-the-third-generation-sequencing-technologies <![CDATA[DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies]]> DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

Our work is published in Scientific Reports:

Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies. Sci. Rep. 6, 31900; doi: 10.1038/srep31900 (2016).

http://www.nature.com/articles/srep31900

The manual can be downloaded from:

https://github.com/yechengxi/DBG2OLC/raw/master/Manual.docx

To use precompiled versions,please go to:

https://github.com/yechengxi/DBG2OLC/tree/master/compiled

 

Address of the bookmark: https://github.com/yechengxi/DBG2OLC

]]> 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/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/37512/purecn-copy-number-calling-and-snv-classification-using-targeted-short-read-sequencing Thu, 09 Aug 2018 04:09:37 -0500 https://bioinformaticsonline.com/bookmarks/view/37512/purecn-copy-number-calling-and-snv-classification-using-targeted-short-read-sequencing <![CDATA[PureCN: copy number calling and SNV classification using targeted short read sequencing]]> This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

Author: Markus Riester [aut, cre], Angad P. Singh [aut]

Maintainer: Markus Riester <markus.riester at novartis.com>

Citation (from within R, enter citation("PureCN")):

Riester M, Singh A, Brannon A, Yu K, Campbell C, Chiang D, Morrissey M (2016). “PureCN: Copy number calling and SNV classification using targeted short read sequencing.” Source Code for Biology and Medicine, 11, 13. doi: 10.1186/s13029-016-0060-z.

Address of the bookmark: http://bioconductor.org/packages/release/bioc/html/PureCN.html

]]> Jit https://bioinformaticsonline.com/bookmarks/view/26923/quast-quality-assessment-tool-for-genome-assemblies Wed, 06 Apr 2016 18:23:33 -0500 https://bioinformaticsonline.com/bookmarks/view/26923/quast-quality-assessment-tool-for-genome-assemblies <![CDATA[QUAST: quality assessment tool for genome assemblies]]> QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.
It can works both with and without a given reference genome.
The tool accepts multiple assemblies, thus is suitable for comparison.

More at http://bioinf.spbau.ru/quast

http://bioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long

]]> Jitendra Prajapati https://bioinformaticsonline.com/bookmarks/view/27094/smash-an-alignment-free-method-to-find-and-visualise-rearrangements-between-pairs-of-dna-sequences Tue, 26 Apr 2016 12:18:49 -0500 https://bioinformaticsonline.com/bookmarks/view/27094/smash-an-alignment-free-method-to-find-and-visualise-rearrangements-between-pairs-of-dna-sequences <![CDATA[Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences]]> Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For visualisation, Smash outputs a SVG image, with an ideogramoutput architecture, where the patterns are represented with several HSV values (only value varies). The method can perform both in small- and large-scale. Nevertheless is more directed to large-scale since that the main aim of the research is to know where the large-scale [chromosomal by chromosome] of several primates was equal/different, having at a glance a map of the entire genomes.

Address of the bookmark: http://bioinformatics.ua.pt/software/smash/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/29992/spines Mon, 28 Nov 2016 05:33:26 -0600 https://bioinformaticsonline.com/bookmarks/view/29992/spines <![CDATA[Spines]]> Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation etc.), as well as specialized tool sets for various analyses. It also features three sequence alignment packages: Satsuma, a highly parallelized program for high-sensitivity, genome-wide synteny; Papaya, an all-purpose alignment tool for less diverged sequences; and SLAP, a context-sensitive local aligner for diverged sequences with large gaps.

Access Spines here.

Address of the bookmark: https://www.broadinstitute.org/genome-sequencing-and-analysis/spines

]]> Jit https://bioinformaticsonline.com/bookmarks/view/30701/harvest Tue, 31 Jan 2017 10:57:56 -0600 https://bioinformaticsonline.com/bookmarks/view/30701/harvest <![CDATA[Harvest]]> Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

_images/screen.png

Tools

  • Parsnp - Core-genome alignment and analysis
  • Gingr - Interactive visualization of alignments, trees and variants
  • HarvestTools - Archiving and postprocessing

Citation

Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology, 15 (11), 1-15 [PDF]

Address of the bookmark: http://harvest.readthedocs.io/en/latest/index.html

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