<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37672?offset=10 https://bioinformaticsonline.com/bookmarks/view/34493/plast-a-fast-accurate-and-ngs-scalable-bank-to-bank-sequence-similarity-search-tool Fri, 01 Dec 2017 04:10:54 -0600 https://bioinformaticsonline.com/bookmarks/view/34493/plast-a-fast-accurate-and-ngs-scalable-bank-to-bank-sequence-similarity-search-tool <![CDATA[PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool]]> PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms.

Relying on unique software architecture, PLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.

PLAST stands for Parallel Local Sequence Alignment Search Tool and is was published in BMC Bioinformatics.

PLAST is a general purpose sequence comparison tool providing the following benefits:

  • PLAST is a high-performance sequence comparison tool designed to compare two sets of sequences (query vs. reference),
  • Reduces the processing time of sequences comparisons while providing highest quality results,
  • Contains a fully integrated data filtering engine capable of selecting relevant hits with user-defined criteria (E-Value, identity, coverage, alignment length, etc.),
  • Does not require any additional hardware, since it is a software solution. It is easy to install, cost-effective, takes full advantage of multi-core processors and uses a small RAM footprint,
  • Ready to be used on desktop computer, cluster, cloud as well as within distributed system running Hadoop.

https://plast.inria.fr/

Address of the bookmark: https://plast.inria.fr/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44508/a-web-based-tool-for-sequence-alignment-statistics-and-innovative-visualization Thu, 04 Apr 2024 01:44:50 -0500 https://bioinformaticsonline.com/bookmarks/view/44508/a-web-based-tool-for-sequence-alignment-statistics-and-innovative-visualization <![CDATA[A web-based tool for sequence alignment statistics and innovative visualization]]> AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA results. Whencompared to currently available tools, AlignStatPlot provides a robust ability to handle andvisualise diversity data, while the online version will save time and encourage researchersto focus on explaining their findings. It is a simple tool that can be used in conjunction withpopulation genetics software (PDF) AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.

Address of the bookmark: https://bioinformatics.um6p.ma/AlignStatPlot/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/41146/lofreq-a-sequence-quality-aware-ultra-sensitive-variant-caller-for-ngs-data Tue, 18 Feb 2020 03:24:22 -0600 https://bioinformaticsonline.com/bookmarks/view/41146/lofreq-a-sequence-quality-aware-ultra-sensitive-variant-caller-for-ngs-data <![CDATA[LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data]]> LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

https://github.com/CSB5/lofreq

http://csb5.github.io/lofreq/installation/

https://github.com/CSB5/lofreq/tree/master/dist

Address of the bookmark: http://csb5.github.io/lofreq/

]]> BioStar https://bioinformaticsonline.com/news/view/41562/submit-your-sars-cov-2-sequence-data-to-genbank Thu, 09 Apr 2020 18:28:25 -0500 https://bioinformaticsonline.com/news/view/41562/submit-your-sars-cov-2-sequence-data-to-genbank <![CDATA[Submit your SARS-CoV-2 sequence data to GenBank]]> Submit your SARS-CoV-2 sequence data to GenBank and SRA with our new submission landing page. Submission is simple and streamlined *and* there’s a rapid turnaround. https://submit.ncbi.nlm.nih.gov/sarscov2/
 
Quickly and easily add your SARS-CoV-2 sequence data to the growing public archive with new, special features and support from NCBI. new SARS-CoV-2 sequence submission landing page will help you get started. GenBank submissions are accessioned and released in approximately 1-2 working days, and Sequence Read Archive (SRA) submissions typically processed and released within hours. Submission is simple!
]]> Neel https://bioinformaticsonline.com/bookmarks/view/38304/lordfast-sensitive-and-fast-alignment-search-tool-for-long-noisy-read-sequencing-data Tue, 27 Nov 2018 04:43:57 -0600 https://bioinformaticsonline.com/bookmarks/view/38304/lordfast-sensitive-and-fast-alignment-search-tool-for-long-noisy-read-sequencing-data <![CDATA[lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data]]> lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads and application.

lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher sensitivity than the available alternatives, it is also among the fastest and has a very low memory footprint.

 

Address of the bookmark: https://github.com/vpc-ccg/lordfast

]]> BioJoker https://bioinformaticsonline.com/bookmarks/view/27331/andi Fri, 13 May 2016 05:16:35 -0500 https://bioinformaticsonline.com/bookmarks/view/27331/andi <![CDATA[Andi]]> This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

This readme covers all necessary instructions for the impatient to get andi up and running. For extensive instructions please consult the manual.

More at https://github.com/evolbioinf/andi/

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2015/01/13/bioinformatics.btu815.full

]]> Jit https://bioinformaticsonline.com/bookmarks/view/33942/mulan-multiple-sequence-local-alignment-and-conservation-visualization-tool Thu, 20 Jul 2017 08:02:32 -0500 https://bioinformaticsonline.com/bookmarks/view/33942/mulan-multiple-sequence-local-alignment-and-conservation-visualization-tool <![CDATA[Mulan: MUltiple sequence Local AligNment and conservation visualization tool]]> Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It combines refine and tba tools to align either "draft" or "finished" quality sequences. Mulan provides a dynamic graphical interface to align and visualize conservation profiles for evolutionarily distant and closely related species.

Input formats, automated data upload from the UCSC Genome Browser, gene annotation, annotation of repetitive elements, and progress report were previously described in the zPicture instructions and we refer the users to these materials for more details. This introduction is mainly focused on some novel features unique to the Mulan.

Address of the bookmark: https://mulan.dcode.org/mulanInstructions.php

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/34734/smash-an-alignment-free-tool-to-find-and-visualise-rearrangements-between-pairs-of-dna-sequences Thu, 21 Dec 2017 08:26:57 -0600 https://bioinformaticsonline.com/bookmarks/view/34734/smash-an-alignment-free-tool-to-find-and-visualise-rearrangements-between-pairs-of-dna-sequences <![CDATA[SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences]]> SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typically 20). The method has been approached with a tool (also called SMASH). For visualization, SMASH outputs a SVG image, with an ideogram output architecture, where the patterns are represented with several HSV values (only value varies). The following image, illustrating the information maps between human and chimpanzee for the several chromosomes, depicts an example:

ScreenShot

 

 

Address of the bookmark: https://github.com/pratas/smash

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34488/scripts-for-the-analysis-of-hgt-in-genome-sequence-data Wed, 29 Nov 2017 16:44:10 -0600 https://bioinformaticsonline.com/bookmarks/view/34488/scripts-for-the-analysis-of-hgt-in-genome-sequence-data <![CDATA[Scripts for the analysis of HGT in genome sequence data.]]> Scripts for the analysis of HGT in genome sequence data

Address of the bookmark: https://github.com/reubwn/hgt

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36271/heap-a-highly-sensitive-and-accurate-snp-detection-tool-for-low-coverage-high-throughput-sequencing-data Thu, 19 Apr 2018 08:06:03 -0500 https://bioinformaticsonline.com/bookmarks/view/36271/heap-a-highly-sensitive-and-accurate-snp-detection-tool-for-low-coverage-high-throughput-sequencing-data <![CDATA[Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data]]> Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both end of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html).

Address of the bookmark: https://github.com/meiji-bioinf/heap

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