<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/27261?offset=560 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/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/opportunity/view/19544/sau-bioinformaticsplant-biotech-jrf-vacancy Fri, 12 Dec 2014 21:27:12 -0600 <![CDATA[SAU Bioinformatics/Plant Biotech JRF Vacancy]]> Applications are invited for the post of Junior Research Fellow (JRF) to work on SERB, DST funded project entitled “Genome wide analysis of ascorbate oxidase multi-gene family and elucidating its role in negative regulation of stress response in rice” under the supervision of Dr. Ananda Mustafiz, Faculty of Life Sciences and Biotechnology, South Asian University.

Qualification: Highly motivated M.Sc. (Bioinformatics/ Biotechnology/ Life Sciences/ Botany/ Agriculture) students are encouraged to apply. Prior experience in Bioinformatics/Plant tissue culture work is preferable. Preferences would be given to DBT/ CSIR / UGC NET qualified students.

Application Procedure: A detailed CV indicating name, date of birth, address, contact number, e-mail address, educational qualifications, NET qualified or not, research experiences if any, should be e-mailed to This email address is being protected from spambots. You need JavaScript enabled to view it. on or before 24th December 2014.

Important Note: Only short listed candidates will be called for interview at Akbar Bhawan, Chanakyapuri, New Delhi. No TA/DA will be paid for attending the interview. SAU Selection Committee reserves the rights to relax any of the qualifications in case the candidate is found otherwise well qualified. The above- mentioned post is temporary and will be initially offered for a period of one year, which can be extended to one more year.

Advertisement: www.sau.ac.in/recruitment/vacancy.html

]]> 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/19635/walk-in-interview-for-research-associate-studentship-and-traineeship-at-bif-nehu-tura-campus Thu, 18 Dec 2014 11:02:05 -0600 <![CDATA[Walk in interview for Research Associate, Studentship and Traineeship at BIF, NEHU, Tura Campus]]> BIOINFORMATICS INFRASTRUCTURE FACILITY (BIF)
Department of RDAP
North-Eastern Hil University, Tura Campus
Tura-79402, Meghalaya

Walk in interview for Research Associate, Studentship and Traineeship at BIF

Applications are invited for the Post of Research Associate, Traineeship and Studentship in the DBT sponsored Bioinformatics Infrastructure Facility (BIF) at the Bioinformatics Centre, Department of RDAP, North-Eastern Hil University, Tura Campus, Tura-79402, Meghalaya. The Posts are purely temporary and terminable at any time without prior notice or assigning any reason thereof. The person engaged, shall not be entailed for any claim implicit or explicit for permanent absorption in the University.

Research Associate- 01

Essential Qualification: M.Sc. in Bioinformatics/Biotechnology from a recognized University/ institute.

Desirable: PhD or Pursuing PhD in the relevant subject(s) or equivalent published work in reputed peer reviewed journals or Advance PG diploma in Bioinformatics courses.

Duties: Creation of database, web designing, maintenance of internet, training of students in Bioinformatics, handling and knowledge of Bioinformatics software tools and technique, conducting Bioinformatics based research and other day to day laboratory work, writing report and scientific papers.

Pay:Rs. 2,00/- + Admissible 10% HRA per month

Age: Below 35 years

Traineeship- 02

Students who have completed Masters Degree in Bioinformatics/Biotechnology or any branch of Life Sciences/Agricultural Sciences/Computer Science to cary out a project work in Bioinformatics.

Desirable: Prior Knowledge of programming languages such as C, JAVA, MySQL is preferable.

Stipend: Rs. 800/- p.m. fixed. Purely temporary for a period of six months.

Studentship: 02

Students pursuing postgraduate degree in Bioinformatics/biotechnology/Agricultural Sciences or any branch of Life Science

Desirable: Prior knowledge of bioinformatics/ programming language is preferable.

Stipend: 800/- p.m. fixed. Purely temporary for a period of six months.

Candidates must send the detailed Biodata via mail/post and bring al the relevant documents in original and one set of attested photocopies of the same at the time of interview. No TA/DA will be paid for attending the interview and candidates have to make their own arrangements.

Last date for receiving application by mail or by post: 16.02.2014

Contact Information:
Dr.B.K. Mishra
Cordinator BIF,
RDAP Department, NEHU, Tura Campus
Phone: 91-03651-23107
Fax: 91-03651-23953
E-mail: drbkm1972@yaho.co.in, birendramishra14@gmail.com

Advertisement: http://www.nehu.ac.in/Advertisements/BIF_TuraAdtvPV_171214.pdf

]]> 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/19597/assistant-professor-at-gauhati-university-guwahati Tue, 16 Dec 2014 01:15:30 -0600 <![CDATA[Assistant Professor at GAUHATI UNIVERSITY, GUWAHATI]]> Advt. No.T/2014/4

Ref. No. GU/Estt/T/308(VI)/2014/6451-61

Applications are invited from the Indian citizens for five (5) teaching posts of Assistant Professor (Contractual) under various departments of Gauhati University. Details of the advertisement, other terms and conditions and the application forms are available in the University website www.gauhati.ac.in

Asstt. Professor (Contractual)

2. M.Sc. Microbiology Course in Botany

3 1.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biochemistry (1 post). (Preference will be given to candidates having experience in Biochemistry).

2.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biotechnology(1 post). (Preference will be given to candidates having experience in Bioinformatics).

3.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biotechnology(1 post). (Preference will be given to candidates having experience in Microbial Genetics).

As per UGC norms

Pay Band & Academic Grade Pay : (Consolidated pay) : Rs. 21,600/- per month

Application Form : Prescribe application form may download from the G.U. website www.gauhati.ac.in

Last date of receipt of filled-in application is 08.01.2015.

Advertisement: www.gauhati.ac.in/openfile.php?file=Notice1258.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/19695/china-university-of-macau-phd-position-2015-in-bioinformatics-computer-science Mon, 22 Dec 2014 00:12:49 -0600 <![CDATA[China University of Macau PhD Position 2015 in Bioinformatics, Computer Science]]> The Computational Biology and Bioinformatics Group at the University of Macau is inviting applications for PhD Position. Applicants will work on a research project focusing on the flexible receptor protein-ligand docking algorithms for computer-aided drug design. The candidate will be working as part of a team in developing novel metaheuristic algorithms and scoring functions for large-scale, highly flexible protein-ligand docking problems. The duration of this PhD position is 2-3 years, starting in August 2015. Remuneration paid to candidate is MOP 11000-14000/month (~USD 1375-1750/month). The applications should be submitted before March 2015.

Study Subject(s): PhD position is award in the field of Bioinformatics/Computer Science.
Course Level: Position is available for pursuing PhD degree level at the University of Macau.
Scholarship Provider: University of Macau
Scholarship can be taken at: China

Eligibility: The ideal candidate would be a master degree holder in Bioinformatics or related disciplines with knowledge in Medical sciences or Life sciences (with GPA of at least 3.0 on a 4-point scale or equivalent) . Knowledge in programming (C and C++) and Linux scripting are necessary; experience in molecular docking, molecular dynamics simulations or molecular modeling is an advantage. The candidate should be fluent in spoken and written English; preference will be given to applicants with good publication records in relevant areas.

Scholarship Open for International Students: Researchers from China can apply for this PhD position.

Scholarship Description:

The Computational Biology and Bioinformatics Group at the University of Macau is looking for a motivated PhD student in Bioinformatics or Computer Science to work on a research project focusing on the flexible receptor protein-ligand docking algorithms for computer-aided drug design. The candidate will be working as part of a team in developing novel metaheuristic algorithms and scoring functions for large-scale, highly flexible protein-ligand docking problems.

Number of award(s): There is only one PhD position available.

Duration of award(s): The duration of this PhD position is 2-3 years.

What does it cover? Remuneration paid to candidate is MOP 11000-14000/month (~USD 1375-1750/month).

Selection Criteria: Not Known

Notification: Not Known

How to Apply: Send your current CV, your academic transcripts, a letter of motivation and research interests, two letters of recommendations from academic faculty to Dr. Shirley Siu at shirleysiu[at]umac.mo before March 2015.

Scholarship Application Deadline: The applications should be submitted before March 2015.

]]> https://bioinformaticsonline.com/bookmarks/view/40972/deepbinner-a-signal-level-demultiplexer-for-oxford-nanopore-reads Mon, 10 Feb 2020 02:45:53 -0600 https://bioinformaticsonline.com/bookmarks/view/40972/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.

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

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