BOL: Related items

NextDenovo: string graph-based de novo assembler for TGS long reads

Jit — Sun, 05 Jan 2020 04:08:29 -0600

NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate is about 97-98%, to further improve single base accuracy, please use NextPolish.

NextDenovo contains two core modules: NextCorrect and NextGraph. NextCorrect can be used to correct TGS long reads with approximately 15% sequencing errors, and NextGraph can be used to construct a string graph with corrected reads. It also contains a modified version of minimap2 for adapting input and output and producing more sensitive and accurate dovetail overlaps, and some useful utilities (see here for more details).

Address of the bookmark: https://github.com/Nextomics/NextDenovo

Walk in for Research Asst & Programmer Enterovirus Research Centre Mumbai - India

Tue, 14 Apr 2015 12:36:51 -0500

Enterovirus Research Centre Mumbai Jobs 2015 –

Walk in for Research Asst & Programmer Posts: Enterovirus Research Centre, Mumbai, Indian Council of Medical Research has issued notification for the recruitment of Research Asst & Programmer vacancies on temporary basis for the project entitled “An Atlas of Non-Polio Enterovirus Types Isolated from Cases of Acute Flaccid Paralysis in India”. Eligible candidates may walk in on 20-04-2015 from 10:00 AM to 12:00 Noon. Other details like age limit, educational qualification, how to apply are given below…

Enterovirus Research Centre Mumbai Vacancy Details:
Total No. of Posts: 04
Name of the Posts:
1. Research Assistant: 03 Posts
2. Programmer: 01 Post

Age Limit: Candidates age should below 28 years. Age relaxations are applicable as per rules.

Educational Qualification: Candidates should have M.Sc (1st Class) in Microbiology/ Bioinformatics/ Biotechnology/ Life Science for post 1, BE/ B.Tech/ MCA for post 2.

Selection Process: Candidates are selected based on their performance in interview.

How to Apply: Eligible candidates may attend for interview along with original certificates, CV, attested copies of relevant certificates, one recent passport size photograph duly affixed on right side of application at Enterovirus Research Centre, Mumbai, Indian Council of Medical Research, Haffkine Institute Cmpound, Acharya Donde Marg, Parel, Mumbai-400012 on 20-04-2015 from 10:00 AM to 12:00 Noon.

Important Dates:
Date & Time of Interview: 20-04-2015 from 10:00 AM to 12:00 Noon.
Registration Time: 12:00 Noon.

Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads

Jit — Mon, 10 Feb 2020 02:45:53 -0600

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

BINC Sample Question Paper !!!

Jitendra Narayan — Thu, 16 Apr 2015 09:15:09 -0500

BINC sample question paper round THREE ...

SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins

BioStar — Mon, 17 Aug 2020 05:25:10 -0500

SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. Thus, SqueezeMeta features several unique characteristics:

Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome
Co-assembly of a large number of metagenomes via merging of individual metagenomes
Includes binning and bin checking, for retrieving individual genomes
The results are stored in a database, where they can be easily exported and shared, and can be inspected anywhere using a web interface.
Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot potential chimeras.
Metatranscriptomic support via mapping of cDNA reads against reference metagenomes

Address of the bookmark: https://github.com/jtamames/SqueezeMeta

Senior Research Fellow (SRF) Bioinformatics at Central Institute for Research on Buffaloes

Sat, 18 Apr 2015 04:30:47 -0500

Senior Research Fellow (SRF) Bioinformatics at Central Institute for Research on Buffaloes
Address: Central Institute for Research on Buffaloes, Sirsa Road, Hisar
State: Haryana
Pay Scale: Post Graduate in subjects other than Veterinary Science Rs. 16000/- per month for 1st and 2nd year and Rs. 18000/- per month for 3rd year. Post Graduate in Veterinary Science Rs. 18000/- per month for 1st and 2nd Year and Rs. 20000/- per month for 3rd year.
Educational Requirements: Master’s degree in biotechnology/animal biotechnology, veterinary/animal biochemistry, veterinary microbiology or veterinary/animal physiology/Nano Technology/Bioinformatics or related area.
Qualifications: Ph.D in relevant field/experience of working in any research project
Details will be available at: http://www.cirb.res.in/attachments/195_Walk-in-Interview%20for%20Senior%20Research%20Fellow%20%28SRF%29%20%28On%20Dated%2020.4.2015%29.pdf
How To Apply: Interested candidates who fulfill the above conditions should report for interview with a copy of their bio-data, photocopy and original certificates and testimonials, other related material i.e. reports, documents, articles, etc., if any.
Date & Time of Interview: 20.04.2015 at 11.00 hrs
Venue: CIRB, Hisar

AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads

Rahul Nayak — Sun, 14 Mar 2021 09:42:47 -0500

AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome.

More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/6146772

Address of the bookmark: https://github.com/huangs001/AlignGraph2

Savitribai Phule Pune University Recruitment for 04 JRF Post in April 2015

Mon, 27 Apr 2015 20:28:59 -0500

Savitribai Phule Pune University announced application for recruitment to the post of Junior Research Fellow. The candidates for the post can apply through prescribed format before 10 May 2015.
Description:

Important Date & Details

Closing Date for Registration: 10 May 2015

Details of Post

Name of Post: Junior Research Fellow- 04 Posts

Pay Scale: Rs. 12,000 or 16,00+ HRA Post Graduate degree with NET (16,000+HRA) Post Graduate Degree (12,000+HRA)

Eligibility Criteria: M.Sc. in Microbiology/Marine Microbiology/ Marine Biotechnology/Biotechnology/Bioinformatics/Zoology or equivalent degree with minimum 60% marks or equivalent grade

Age Limit- Not more than 28 years

Organisation Name: Savitribai Phule Pune University
Eligibility for the post:

Selection Procedure: The selection procedure is through personal interview. No TA/DA will be paid for appearing in the interview.

How to Apply: The candidates may send their application along with CV to the Head Department of Zoology, Savitribai Phule University on or before 10 May 2015.

Steps to find palindrome in genomes !

BioStar — Thu, 09 Mar 2023 02:56:54 -0600

Palindromes are sequences of nucleotides that read the same backward as forward. They can be present in genomes and have various biological functions. Here are some methods for discovering palindromes in genomes:

Direct sequence search: One of the simplest ways to discover palindromes is to search the genome sequence directly for palindromic sequences using pattern matching tools, such as regular expressions or string algorithms. This approach can be useful for discovering simple palindromes, but may miss more complex palindromic structures.
Dot plot analysis: Dot plot analysis is a graphical method that can be used to identify palindromic regions in a genome. It involves plotting the genome sequence against itself and examining the diagonal patterns that emerge. Palindromic regions will appear as symmetrical patterns along the diagonal.
Restriction enzyme analysis: Some restriction enzymes, such as EcoRI and HindIII, recognize palindromic sequences and cleave DNA at these sites. By digesting the genome with these enzymes and examining the resulting fragments, palindromic regions can be identified.
Next-generation sequencing: High-throughput sequencing technologies, such as PacBio and Oxford Nanopore, can generate long reads that can span entire palindromic regions. By mapping these reads to the genome, palindromic regions can be identified and characterized.
Comparative genomics: Comparing the genomes of related species can also reveal palindromic regions that are conserved across evolutionarily divergent lineages. This approach can help identify functional palindromes that are under selective pressure.

Overall, the discovery of palindromic sequences in genomes can be accomplished using a variety of methods, each with their own advantages and limitations. A combination of these methods can provide a comprehensive understanding of the palindromic landscape of a genome.

HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning

Abhimanyu Singh — Tue, 01 Jan 2019 12:01:00 -0600

HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read alignments.

HECIL’s core algorithm by introducing an iterative learning paradigm that enhances the correction policy at each iteration by incorporating knowledge gathered from previous iterations via data-driven confidence metrics assigned to prior corrections.

Address of the bookmark: https://github.com/NDBL/HECIL