<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/31064?offset=740 https://bioinformaticsonline.com/bookmarks/view/36739/blasr-mapping-single-molecule-sequencing-reads-using-basic-local-alignment-with-successive-refinement-blasr-theory-and-application Wed, 23 May 2018 06:54:32 -0500 https://bioinformaticsonline.com/bookmarks/view/36739/blasr-mapping-single-molecule-sequencing-reads-using-basic-local-alignment-with-successive-refinement-blasr-theory-and-application <![CDATA[BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): Theory and Application,]]> BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion error.

Here is how I use the blasr to align PacBio reads to the contigs (target.fasta). The “target.fasta.sa” is the suffix array from “target.fasta” generated by sawriter.

blasr query.fa ./target.fasta -sa ./target.fasta.sa -bestn 40 -maxScore -500 -m 4 -nproc 24 -out target.m4 -maxLCPLength 15

the output format option “-m 4″ generate the alignment coordinate. Not fully documented, but I can explain that to you. 

I use a 24 cores / 48G ram server for the alignment. It took about 2 to 3 hours aligning 3G PacBio Reads to 10^6 sequences of short read contigs with a mean 3.5kbp length.

Address of the bookmark: http://bix.ucsd.edu/projects/blasr/

]]> Jit https://bioinformaticsonline.com/blog/view/30874/important-journals-blogs-and-forums-for-bioinformaticians Wed, 08 Feb 2017 09:15:31 -0600 https://bioinformaticsonline.com/blog/view/30874/important-journals-blogs-and-forums-for-bioinformaticians <![CDATA[Important Journals, Blogs and Forums for Bioinformaticians]]> Journals. Most journals have RSS feeds for their current updates.

Blogs. Some of these blogs are very relevant to bioinfo jobs. Others are more personal interest.

  • Variance Explained: David Robinson’s blog (Data Scientist at Stack Overflow, works in R and Python).
  • Global Biodefense: News on pathogens, outbreaks, and preparedness, with periodic posts on genomics and bioinformatics-related developments and funding opportunities.
  • In between lines of code: Lex Nederbragt’s blog on biology, sequencing, bioinformatics, …
  • Simply Statistics: A statistics blog by Rafa Irizarry, Roger Peng, and Jeff Leek.
  • Bits of DNA: Reviews and commentary on computational biology by Lior Pachter (fair warning: dialogue here can get a bit heated!).
  • Blue Collar Bioinformatics: articles related tool validation and the open source bioinformatics community.
  • Microbiome Digest – Bik’s Picks: A daily digest of scientific microbiome papers, by Elisabeth Bik, Science Editor at uBiome.
  • Living in an Ivory Basement: Titus Brown’s blog on metagenomics, open science, testing, reproducibility, and programming.
  • Enseqlopedia: James Hadfield’s blog on all things NGS.
  • Epistasis Blog: Jason Moore’s computational biology blog.
  • RStudio Blog: announcements about new RStudio functionality, updates about the tidyverse, and more.
  • nextgenseek.com: Next-Gen Sequencing Blog covering new developments in NGS data & analysis.
  • RNA-Seq Blog: Transcriptome Research & Industry News.
  • The Allium: We all need a little humor in our lives. Like The Onion, but for science.

Forums.

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43795/anchorwave Wed, 23 Feb 2022 08:14:35 -0600 https://bioinformaticsonline.com/bookmarks/view/43795/anchorwave <![CDATA[AnchorWave]]> AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor intervals. By performing sensitive sequence alignment for each shorter interval via a 2-piece affine gap cost strategy and merging them together, AnchorWave generates a whole-genome alignment for each collinear block. AnchorWave implements commands to guide collinear block identification with or without chromosomal rearrangements and provides options to use known polyploidy levels or whole-genome duplications to inform alignment.

Address of the bookmark: https://github.com/baoxingsong/AnchorWave

]]> Neel https://bioinformaticsonline.com/opportunity/view/30928/jrf-bioinformatics-job-vacancies-in-tezpur-university Tue, 14 Feb 2017 16:40:26 -0600 <![CDATA[JRF Bioinformatics job vacancies in Tezpur University]]> Memo No. DoRD/CSE/SSS/20-295/112-A Date: 01/02/2017

Project Title : “Integrating genome scale metabolic analysis of model plant pathogen Ralstonia solanacearum with RNAseq and fluxomics”

Essential qualification : M.Tech. in CSE/IT (With specialization in Computational Biology/Bioinformatics) or M.Sc. in Bioinformatics/Biosciences/Molecular Biology Biotechnology preferably with NET/GATE/BET. Candidates should have minimum 55 % mark both in 10th and 10+2 Science examinations and mathematics at 10+2 Science. Desirable: Preference will be given to the candidates having experience in computational analysis of genome sequences or similar projects.

No. of Post : 01

Remuneration : Rs. 25,000/- for the 1st two years and Rs. 28,000/- for the 3rd year for SRF and applicable to the candidate having post graduate degree in Basic Science with NET/GATE/BET qualification or post graduate degree in professional course. Rs. 12,000/- for the 1st two years and Rs. 14,000/- for the 3 rd year for SRF,

Age : 28 years

Duration : Three (03) years or till completion of the project or until further order, whichever is earlier.

Hiring Process : Walk - In
Job Role: Research/JRF/SRF

Walk-in-interview will be held on 17th February, 2017, 11.15 a.m. at the office of the Head, Department of Computer Science and Engineering, Tezpur University.

Interested candidates may appear before the interview board with original documents from 10th standard onwards and photocopies of mark sheets, certificates, testimonials, caste certificate (if applicable), experience certificate certificates of NET/GATE/BET or similar examination qualifications, any other testimonials and a copy of recent curriculum vitae (CV) on the day of interview.

More at http://www.tezu.ernet.in/ProjectWalkin/Advt-DoRD-CSE-SSS-20-295-112-A.pdf

]]> https://bioinformaticsonline.com/bookmarks/view/44559/metagraph-ultra-scalable-framework-for-dna-search-alignment-assembly Sat, 08 Jun 2024 16:15:25 -0500 https://bioinformaticsonline.com/bookmarks/view/44559/metagraph-ultra-scalable-framework-for-dna-search-alignment-assembly <![CDATA[MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly]]> The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle, transforming single input samples into error-removed, refined sample graphs, which are then merged into a joint metagraph index. Each input sample is annotated in the joint index as a subgraph. This graph index enriched with metadata can then be used for downstream applications such as sequence search or differential assembly.

Searcg link https://metagraph.ethz.ch/search 

Pre-print https://www.biorxiv.org/content/10.1101/2020.10.01.322164v4 

Address of the bookmark: https://metagraph.ethz.ch/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/33955/crocoblast-optimized-parallel-implementation-of-local-sequence-alignment-algorithms Tue, 25 Jul 2017 05:03:10 -0500 https://bioinformaticsonline.com/bookmarks/view/33955/crocoblast-optimized-parallel-implementation-of-local-sequence-alignment-algorithms <![CDATA[CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms]]> Local sequence alignment is a cornerstone of bioinformatics, allowing to compare the amino-acid sequences of different proteins, or the nucleotide sequences of different pieces of DNA. The Basic Local Alignment Search Tool (BLAST) has revolutionized the field of bioinformatics, and is currently implemented in all free and commercial bioinformatics packages. However, with the advent of Next Generation Sequencing (NGS) and the development of new sequencing techniques, the utility of traditional BLAST implementations is limited. CrocoBLAST combines the accuracy and general applicability of BLAST with computational efficiency, accessibility, and user experience, so that NGS data can be analyzed efficiently even when only modest computational resources are available.

https://webchem.ncbr.muni.cz/Platform/App/CrocoBLAST

Address of the bookmark: https://webchem.ncbr.muni.cz/Platform/App/CrocoBLAST

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36800/genomemapper-simultaneous-alignment-of-short-reads-against-multiple-genomes Fri, 25 May 2018 09:29:44 -0500 https://bioinformaticsonline.com/bookmarks/view/36800/genomemapper-simultaneous-alignment-of-short-reads-against-multiple-genomes <![CDATA[GenomeMapper: Simultaneous alignment of short reads against multiple genomes]]> Address of the bookmark: http://1001genomes.org/software/genomemapper.html

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37502/alignqc-a-tool-for-assessing-an-alignment-and-generating-reports-that-are-easy-to-share Tue, 07 Aug 2018 04:41:07 -0500 https://bioinformaticsonline.com/bookmarks/view/37502/alignqc-a-tool-for-assessing-an-alignment-and-generating-reports-that-are-easy-to-share <![CDATA[AlignQC: A tool for assessing an alignment, and generating reports that are easy to share]]> Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysis results.

https://f1000research.com/articles/6-100/

https://github.com/jason-weirather/AlignQC

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

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37776/rhat-a-seed-and-extension-based-noisy-long-read-alignment-tool Sun, 23 Sep 2018 05:12:22 -0500 https://bioinformaticsonline.com/bookmarks/view/37776/rhat-a-seed-and-extension-based-noisy-long-read-alignment-tool <![CDATA[rHAT: a seed-and-extension-based noisy long read alignment tool]]> rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT) sequencing reads.

Address of the bookmark: https://github.com/dfguan/rHAT

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/31526/sequenceserver Fri, 10 Mar 2017 08:51:55 -0600 https://bioinformaticsonline.com/bookmarks/view/31526/sequenceserver <![CDATA[sequenceserver]]> SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.

More at http://sequenceserver.com.

Address of the bookmark: https://github.com/wurmlab/sequenceserver

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