<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/27973?offset=350 https://bioinformaticsonline.com/bookmarks/view/37574/simlord-a-read-simulator-for-third-generation-sequencing-reads Wed, 22 Aug 2018 10:40:27 -0500 https://bioinformaticsonline.com/bookmarks/view/37574/simlord-a-read-simulator-for-third-generation-sequencing-reads <![CDATA[SimLoRD: A read simulator for third generation sequencing reads]]> SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model.

Reads are simulated from both strands of a provided or randomly generated reference sequence.

  • The reference can be read from a FASTA file or randomly generated with a given GC content. It can consist of several chromosomes, whose structure is respected when drawing reads. (Simulation of genome rearrangements may be incorporated at a later stage.)
  • The read lengths can be determined in four ways: drawing from a log-normal distribution (typical for genomic DNA), sampling from an existing FASTQ file (typical for RNA), sampling from a a text file with integers (RNA), or using a fixed length
  • Quality values and number of passes depend on fragment length.
  • Provided subread error probabilities are modified according to number of passes
  • Outputs reads in FASTQ format and alignments in SAM format

Address of the bookmark: https://bitbucket.org/genomeinformatics/simlord/

]]> Aaryan Lokwani https://bioinformaticsonline.com/opportunity/view/19020/jrf-in-bioinformatics-bioinformatics-centre-north-eastern-hill-university Thu, 06 Nov 2014 10:24:05 -0600 <![CDATA[JRF in Bioinformatics @ Bioinformatics Centre, North-Eastern Hill University]]> Applications with complete bio-data are invited for JRF (3) and Project Assistant (1) in a DBT project "Next Generation Sequencing (NGS)-based de novo assembly of expressed transcripts and genome information of Orchids in North-East India" sanctioned for a period of 3 years.

Details are available at www.nehu.ac.in and www.bicnehu.ac.in.

Applications must reach the undersigned within 15 days from the date of publication of this advertisement.

Prof. Pramod Tandon. PI/Mr. Devendra Kumar Biswal (Co-PI)

]]> https://bioinformaticsonline.com/bookmarks/view/37737/rebaler-program-for-conducting-reference-based-assemblies-using-long-reads Tue, 18 Sep 2018 07:52:41 -0500 https://bioinformaticsonline.com/bookmarks/view/37737/rebaler-program-for-conducting-reference-based-assemblies-using-long-reads <![CDATA[Rebaler: program for conducting reference-based assemblies using long reads.]]> Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences.

I made Rebaler for bacterial genomes (specifically for the task of testing basecallers). It should in principle work for non-bacterial genomes as well, but I haven't tested it.

Address of the bookmark: https://github.com/rrwick/Rebaler

]]> Jit https://bioinformaticsonline.com/news/view/19087/dcgor Sat, 08 Nov 2014 14:54:28 -0600 https://bioinformaticsonline.com/news/view/19087/dcgor <![CDATA[dcGOR]]> An R package for analysing ontologies and protein domain annotations has been published in PLoS Computational Biology (http://dx.doi.org/10.1371/journal.pcbi.1003929). The package is distributed as part of CRAN (http://cran.r-project.org/package=dcGOR), and also at GitHub for version control.

The dedicated website is available in http://supfam.org/dcGOR, from which several demos are also provided:

1. Analysing SCOP domains: http://supfam.org/dcGOR/demo-Fang.html

2. Analysing Pfam domains: http://supfam.org/dcGOR/demo-Basu.html

3. Analysing InterPro domains: http://supfam.org/dcGOR/demo-Customisation.html

 

]]> Martin Jones https://bioinformaticsonline.com/bookmarks/view/38299/deepbinner-a-signal-level-demultiplexer-for-oxford-nanopore-reads Tue, 27 Nov 2018 03:38:49 -0600 https://bioinformaticsonline.com/bookmarks/view/38299/deepbinner-a-signal-level-demultiplexer-for-oxford-nanopore-reads <![CDATA[Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads]]> Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful in image classification. Unlike other demultiplexers (e.g. Albacore and Porechop), Deepbinner identifies barcodes from the raw signal (a.k.a. squiggle) which gives it greater sensitivity and fewer unclassified reads.

  • Reasons to use Deepbinner:
    • To minimise the number of unclassified reads (use Deepbinner by itself).
    • To minimise the number of misclassified reads (use Deepbinner in conjunction with Albacore demultiplexing).
    • You plan on running signal-level downstream analyses, like Nanopolish. Deepbinner can demultiplex the fast5 fileswhich makes this easier.
  • Reasons to not use Deepbinner:
    • You only have basecalled reads not the raw fast5 files (which Deepbinner requires).
    • You have a small/slow computer. Deepbinner is more computationally intensive than Porechop.
    • You used a sequencing/barcoding kit other than the ones Deepbinner was trained on.

Address of the bookmark: https://github.com/rrwick/Deepbinner

]]> Neel https://bioinformaticsonline.com/opportunity/view/19162/icgeb-bioinformatics-rasrfjrf-vacancies Thu, 13 Nov 2014 13:39:30 -0600 <![CDATA[ICGEB Bioinformatics RA/SRF/JRF Vacancies]]> Research Associate/JRF/SRF position, DBT Sponsored Bioinformatics Infrastructure Facility

Applicants should hold a PhD or a first class MSc/MTech degree in Bioinformatics of Biotechnology/Life Sciences; experience in using bioinformatics tools, working in Linux and knowledge of computer network administration.

Submit CV and letter of interest by email to: Dr. Dinesh Gupta atdinesh@icgeb.res.in

]]> https://bioinformaticsonline.com/bookmarks/view/38892/wtdbg2-a-fuzzy-bruijn-graph-approach-to-long-noisy-reads-assembly Mon, 04 Feb 2019 04:53:47 -0600 https://bioinformaticsonline.com/bookmarks/view/38892/wtdbg2-a-fuzzy-bruijn-graph-approach-to-long-noisy-reads-assembly <![CDATA[wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly]]> Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. 

./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo prefix
./wtpoa-cns -t 16 -i prefix.ctg.lay.gz -fo prefix.ctg.fa

Address of the bookmark: https://github.com/ruanjue/wtdbg2

]]> BioStar https://bioinformaticsonline.com/opportunity/view/19540/niab-molecular-biologybioinformatics-scientistra-openings Fri, 12 Dec 2014 21:08:47 -0600 <![CDATA[NIAB Molecular Biology/Bioinformatics Scientist/RA Openings]]> D. No. 1-121/1, 4th and 5th Floors, Axis Clinicals Building, Miyapur, Hyderabad, Telangana, India- 500 049

Email: admin@niab.org.in Telephones: +91 40 2304 9403 Telefax: +91 40 2304 2740
Advertisement No: 5/2014

About NIAB National Institute of Animal Biotechnology (NIAB), Hyderabad, an autonomous institute under the aegis of Department of Biotechnology, Government of India, is aimed to harness novel and emerging biotechnologies and create knowledge in the cutting edge areas for improving animal health and productivity.

Applications are invited for the following temporary research positions to work in ongoing DBTBBSRC sponsored research project entitled “Transcriptome Analysis in Indian buffalo and the Genetics of Innate Immunity” at the National Institute of Animal Biotechnology, Hyderabad.

(A) Project Scientist – Level B (One Position)

Emoluments: Rs. 15600 + GP Rs. 5400 + 30 % HRA p.m. (Total emoluments will be Rs. 49,770/-p.m. for the duration of the project)

Essential Qualification: Candidates having M.V.Sc. in Veterinary Microbiology / Veterinary Pathology / Veterinary Public Health / Ph.D. degree in Life Sciences, Biotechnology, Molecular Biology or any other related field from the recognized university are eligible to apply.

The candidate should have a good academic record and research experience as evidenced from published in standard referred journals / patents.

Desirable: Candidates having research experience in the area of tissue culture, genomics, Transcriptomics and Advanced Molecular Biology will be given preference.

Age Limit: Not exceeding 30 years as on last date of the submission of the application.

(B) Research Associate in Bioinformatics (One position)

Fellowship: Rs. 22,000 + 30 % HRA

Essential Qualification: Candidates having Ph.D. degree or M.Tech. with three years of
experience in Bioinformatics, Computational Biology, Biotechnology, Life Sciences or any other related field are eligible to apply.

Desirable: Candidate having research experience in the area of next generation sequencing (NGS) data analysis, Genome wide association studies, Genomic selection, advance genomic data analysis etc., will be given preference. The candidate should have a good academic record and research experience as evidenced from published papers in standard journals / patents.

Age Limit: Not exceeding 30 years as on last date of the submission of the application.

Project Duration: The duration of the project is Three years and the positions are co- terminus with the duration of the project. (Initial appointment will be for one year and further extension will be granted based on annual review).

Mode of submission of application: Only online applications are to be submitted through
www.niab.org.in on or before 08 December, 2014. Link for online submission of applications will be available from 10 November 2014.

Advertisement: www.niab.org.in/Notifications/Advt_5_2014/Advt_5_2014.pdf

]]> https://bioinformaticsonline.com/bookmarks/view/40701/fastgt-an-alignment-free-method-for-calling-common-snvs-directly-from-raw-sequencing-reads Tue, 28 Jan 2020 03:27:33 -0600 https://bioinformaticsonline.com/bookmarks/view/40701/fastgt-an-alignment-free-method-for-calling-common-snvs-directly-from-raw-sequencing-reads <![CDATA[FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads]]> FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the frequency of k-mers in sequencing data and predicts the genotype. All this takes less than 1 hour on average low-cost Linux server.

http://bioinfo.ut.ee/FastGT/

https://github.com/bioinfo-ut/GenomeTester4/

Address of the bookmark: http://bioinfo.ut.ee/FastGT/

]]> Jit https://bioinformaticsonline.com/opportunity/view/19542/bic-pgi-bioinformatics-project-dissertation-program Fri, 12 Dec 2014 21:17:30 -0600 <![CDATA[BIC-PGI Bioinformatics Project Dissertation Program]]> Biomedical Informatics Centre, PGIMER, Chandigarh invites application for a project dissertation program for students who have completed their first year of M.Sc. in Bioinformatics.

This is an exciting opportunity for Master's students to train in modern methods in Bioinformatics. The duration of the training will be four to six months, starting from January 2015.

Education: Pursuing M.Sc. Bioinformatics

Essential: Post graduate applicants should have completed their first year and should be in the third semester or first half of the second year.

Only students who are willing to spend a minimum period of 4 months to a maximum of six months, without any break, would be eligible for the program.

How to Apply: Candidates interested in the above project dissertation program should apply online.

Send your CV, Scanned copy of letter of recommendation from Head of Institution along with Registration form in the given format should be sent to: info@bicpgi.org

Please mention clearly “Project dissertation & your Name” in the Subject.

The last date for application is December 31, 2014

Note: Selected candidates may please note that the program is free of cost and would not provide any financial aid for transport and stay.

Name of the selected candidates would be posted on the centre website by December 31, 2014. Incomplete applications will be rejected.

For more information visit our website: http://www.bic-pgi.org/project_dissertation.pdf

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