<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/26923?offset=590 https://bioinformaticsonline.com/bookmarks/view/26911/raca-reference-assisted-chromosome-assembly Wed, 06 Apr 2016 09:29:50 -0500 https://bioinformaticsonline.com/bookmarks/view/26911/raca-reference-assisted-chromosome-assembly <![CDATA[RACA: Reference-Assisted Chromosome Assembly]]> Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads.

http://www.ncbi.nlm.nih.gov/pubmed/23307812

http://bioen-compbio.bioen.illinois.edu/RACA/

Address of the bookmark: http://bioen-compbio.bioen.illinois.edu/RACA/

]]> Priya Singh https://bioinformaticsonline.com/bookmarks/view/27257/busco-assessing-genome-assembly-and-annotation-completeness-with-benchmarking-universal-single-copy-orthologs Tue, 10 May 2016 07:46:24 -0500 https://bioinformaticsonline.com/bookmarks/view/27257/busco-assessing-genome-assembly-and-annotation-completeness-with-benchmarking-universal-single-copy-orthologs <![CDATA[BUSCO: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs]]>
  • High-throughput genomics has revolutionized biological research, however, while the number of sequenced genomes grows by the day, quality assessment of the resulting assembled sequences remains complicated and mostly limited to technical measures like N50. 
  • BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. 
  • BUSCO assessments are implemented in open-source software, with comprehensive lineage-specific sets of Benchmarking Universal Single-Copy Orthologs for arthropods, vertebrates, metazoans, fungi, eukaryotes, and bacteria. 
  • These conserved orthologs are ideal candidates for large-scale phylogenomics studies, and the annotated BUSCO gene models built during genome assessments provide a comprehensive gene predictor training set for use as part of genome annotation pipelines. 
  • BUSCO assessments offer intuitive metrics, based on evolutionarily informed expectations of gene content from hundreds of species, to gauge completeness of rapidly accumulating genomic data and satisfy an Iberian's quest for quality - "Busco calidad/qualidade".

    • Address of the bookmark: http://busco.ezlab.org/

    ]]>     Anjana     https://bioinformaticsonline.com/bookmarks/view/27328/platanus Fri, 13 May 2016 05:12:40 -0500 https://bioinformaticsonline.com/bookmarks/view/27328/platanus <![CDATA[Platanus]]> Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of
    highly heterozygous diploids from massively parallel shotgun sequencing data.

    The latest version is 1.2.4.

    To cite Platanus, please use the following:

    Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T, “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads”. Genome Res. 2014 Aug;24(8):1384-95. doi: 10.1101/gr.170720.113. [abstract | full text]

    Address of the bookmark: http://platanus.bio.titech.ac.jp/

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/28805/bambus Tue, 16 Aug 2016 08:09:15 -0500 https://bioinformaticsonline.com/bookmarks/view/28805/bambus <![CDATA[Bambus]]>

    Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

    Address of the bookmark: https://www.cbcb.umd.edu/software/bambus2

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/29957/record Fri, 25 Nov 2016 08:23:36 -0600 https://bioinformaticsonline.com/bookmarks/view/29957/record <![CDATA[RECORD]]> Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome of the species. However, in most typical protocols, this information is disregarded and the reference genome is used. Results. We provide a new approach that allows researchers to reconstruct genomes very closely related to the reference genome (e.g., mutants of the same species) directly from the reads used in the experiment. Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified reference sequence. In this way, it can very quickly, and at no additional sequencing cost, generate new, modified reference sequence that is closer to the actual sequenced genome and has a full coverage. In this paper, we describe our approach and test its implementation called RECORD. We evaluate RECORD on both simulated and real data. We made our software publicly available on sourceforge. Conclusion. Our tests show that on closely related sequences RECORD outperforms more general assisted-assembly software.

    More at https://sourceforge.net/projects/record-genome-assembler/files/

    Address of the bookmark: https://www.ncbi.nlm.nih.gov/pubmed/26558255

    ]]>     Bulbul     https://bioinformaticsonline.com/opportunity/view/30825/open-positions-in-pasini%E2%80%99s-lab Sat, 04 Feb 2017 08:17:18 -0600 <![CDATA[Open Positions in Pasini’s lab]]> Computational Biologists
    Open to PhD-student and Post-doc candidates
    We are looking for wet and computational biologists to work on an ERC funded project in our
    laboratory located at the Department of Experimental Oncology of the European Institute of
    Oncology in Milan (Italy). The project will focus on different aspects of the function of Polycomb
    Group proteins and other chromatin modifying activities in relation to their role in regulating cellular
    identity in the development of adult tissues.
    The candidates will be in charge of computational analysis and data management related to the
    project. She/he will directly interact with the wet scientists working in our laboratory while working
    embedded in the community of computational biologists present at our institution. The work will
    involve the analysis of sequencing data produced with cutting edge technologies to study gene
    expression and chromatin environment including data produced on rare cell populations and single
    cells. The applicants must have a good knowledge of programming in python/perl/java along with
    strong statistical background and performing analysis in R platform. A biological background is
    also recommended however it’s not mandatory for application.
    Each applicant should submit a full CV (with a detailed description of her/his background,
    expertise, achievements and publication records) together with a letter of intent and at least two
    contacts for recommendations (for a post-doc position). Competitive salary will be offered based
    on the experience of the candidate. Non Italian as well as Italian applicants that have been working
    outside Italy (>3yrs.) will have the opportunity to benefit of a full tax deduction for the first three
    years of contract.
    Applications should be submitted as single PDF to diego.pasini@ieo.it

    Lab https://www.ieo.it/en/RESEARCH/People/Researchers/Pasini-Diego/

    ]]>         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/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/31014/sockeye Fri, 17 Feb 2017 08:51:16 -0600 https://bioinformaticsonline.com/bookmarks/view/31014/sockeye <![CDATA[sockeye]]> This sockeye software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization.

    Address of the bookmark: http://www.bcgsc.ca/platform/bioinfo/software/sockeye/releases/1.3

    ]]>     Jit     https://bioinformaticsonline.com/opportunity/view/32227/postdoctoral-research-position-in-bioinformatics-in-milan Thu, 20 Apr 2017 12:53:12 -0500 <![CDATA[Postdoctoral Research Position in Bioinformatics in Milan]]> The lab of Immunobiology of Neurological Disorders has a main interest in the biological processes associated with multiple sclerosis, an inflammatory disorder of the central nervous system. The projects of interest for this application involve research on translational bioinformatics in complex human neurological disorders.

    You have a PhD in Computational Science, Bioinformatics, or equivalent, and expertise in analysis and modeling of human RNA-seq data, statistics, data mining and machine learning. Excellent communication skills in English (written and oral) is a must. Flexibility and willingness to work across multiple projects and technologies in a rapidly evolving scientific context is required.
    Salary will depend on qualification and experience. Starting date: immediate.

    Interested candidates should send to farina.cinthia@hsr.it:

    1. CV (please show evidences of relevant titles, projects, courses, references, etc.)
    2. One page with a list of research topics (i.e. ongoing projects)
    3. earliest availability

    4. 2-3 contact names

    ]]>