BOL: Related items

Research Associate and Junior Research Fellow at North-Eastern Hill University - Tura, Meghalaya

Fri, 28 Oct 2016 09:54:43 -0500

Research Associate and Junior Research Fellow
North-Eastern Hill University - Tura, Meghalaya
₹18,000 a month
Applications are invited for the post of Research Associate and JRF in the DBT sponsored Bioinformatics Infrastructure Facility (BIF), posts are purely temporary and terminable at anytime without prior notice or assigning any reason thereof.

Research Associate :
Essential Qualification: Ph.D in Bioinformatics/Biotechnology/Life Science from a reocngised univeristy/institute
Pay: Rs.36000-/- + Admissible 10% HRA per month
Age: Below 35 years

Junior Research Fellow
Essential Qualification: M.Sc in Bioinformatics/Biotechnology/Life Science from a reocngised univeristy/institute
Pay: Rs.18000-/- + per month
Age: Below 35 years

Last date for receving application by mail or post is 08.11.2016

Company Info.
North-Eastern Hill University

Bioinformatics Infrastructure Facility (BIF) Department of RDAP North-Eastern Hill University, Tura Campus Tura-794002, Meghalaya

More at http://www.nehu.ac.in/Advertisements/BIFTuraManpowerAdvt_25102016.pdf

wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly

BioStar — Mon, 04 Feb 2019 04:53:47 -0600

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

Statistics and probability

Jit — Tue, 08 Nov 2016 07:34:25 -0600

Topics

Displaying and describing data

Modeling distributions of data

Describing relationships in quantitative data

Designing studies

Probability

Random variables

Sampling distributions

Confidence intervals (one sample)

Significance tests (one sample)

Significance tests and confidence intervals (two samples)

Inference for categorical data (chi-square tests)

Advanced regression (inference and tran

Address of the bookmark: https://www.khanacademy.org/math/statistics-probability

Bioistats Online course

Abhimanyu Singh — Thu, 10 Nov 2016 04:22:51 -0600

One of our primary focuses will be to develop an understanding of the various ways in which we can assign a probability to some chance event. We'll also learn the fundamental properties of probability, investigate how probability behaves, and learn how to calculate the probability of a new chance event.

This book is handy understanding basic concepts.

Address of the bookmark: https://onlinecourses.science.psu.edu/stat414/node/287

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

BioStar — Fri, 27 Mar 2020 22:49:31 -0500

HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering.

More at https://www.biorxiv.org/content/10.1101/2020.03.14.992248v3

Address of the bookmark: https://github.com/marbl/canu

Research Officer at National Tea Research Foundation

Fri, 18 Nov 2016 04:19:24 -0600

National Tea Research Foundation (NTRF) a registered body, requires qualified and experienced agricultural research scientist for contractual appointment as per details below :

Post Research Officer, NTRF, Kolkata

Essential Post Graduate degree in Life Science having special paper in Bioinformatics. Post Graduate degree in Bioinformatics.

Desirable Ph. D. in the area of computational biology or bioinformatics.

Job Experience Work experience on database development, capable to work independently and efficient in bioinformatics related project.

Job Responsibility

To develop database on various aspects of tea research.

Screening of the In-house projects of NTRF at the preliminary level.

Review and evaluation of In-house projects of NTRF. Technical monitoring of the In-house projects of NTRF.

Reviewing the final technical report of the In-house projects of NTRF.

Putting-up of same proposals for taking approval and sanction of the competent authority.

Physical and technical verification of the In-house projects of NTRF.

To assist in organizing seminars / workshops / meetings etc.

Interested candidate may appear for walk-in Interview on 17 th November, 2016

More Info :

http://www.teaboard.gov.in/pdf/Recruitment_for_the_post_of_Research_Officer_pdf7538.pdf

Supernova: generates phased, whole-genome de novo assemblies from a Chromium-prepared library.

Jit — Sun, 31 May 2020 01:59:30 -0500

Supernova generates phased, whole-genome de novo assemblies from a Chromium-prepared library.

Please see Achieving Success with De Novo Assembly and System Requirements before creating your Chromium libraries for assembly.

Supernova should be run using 38-56x coverage of the genome.
• Somewhat higher coverage is sometimes advantageous.
• Supernova will exit if it finds that coverage is far from the recommended range.
• Note that at most 2.14 billion reads are allowed.
• Please note that we have not extensively tested genomes larger than human, and any genome above approximately 4 GB should be considered experimental and is not supported.

Address of the bookmark: https://support.10xgenomics.com/de-novo-assembly/software/pipelines/latest/using/running

Spines

Jit — Mon, 28 Nov 2016 05:33:26 -0600

Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation etc.), as well as specialized tool sets for various analyses. It also features three sequence alignment packages: Satsuma, a highly parallelized program for high-sensitivity, genome-wide synteny; Papaya, an all-purpose alignment tool for less diverged sequences; and SLAP, a context-sensitive local aligner for diverged sequences with large gaps.

Access Spines here.

Address of the bookmark: https://www.broadinstitute.org/genome-sequencing-and-analysis/spines

bipype

Jit — Thu, 01 Dec 2016 08:47:38 -0600

Bipype is a very useful program, which prepare a lot of types of bioinformatics analyses. There are three input options: amplicons, WGS (whole genome sequences) and metatranscriptomic data. If amplicons are input data, then bipype does reconstruction and pairs merging. After that biodiversity is searching. There are two types of searching depending on the amplicons types (ITS or 16S). If WGS are chosen, then bipype finds the SA coordinates of the input reads and generates alignments in the SAM format given single-end reads, aligns reads to reference sequence(s). All of these analyses will be shown with Krona program, which allows to show hierarchical data with pie charts.

Address of the bookmark: https://readthedocs.org/projects/bipype/

Spades tutorial PDF

Abhimanyu Singh — Tue, 01 Feb 2022 04:56:43 -0600

SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single-cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole-genome sequencing and metagenomic datasets.