BOL: Related items

SDA: Long-read sequence and assembly of segmental duplications

Jit — Tue, 05 Mar 2019 10:00:57 -0600

Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of long reads corresponding to distinct paralogs.

https://github.com/mvollger/SDA

Address of the bookmark: https://www.nature.com/articles/s41592-018-0236-3

CONTIGuator !

BioStar — Fri, 04 Oct 2019 01:27:58 -0500

CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).

Address of the bookmark: https://sourceforge.net/projects/contiguator/

IMPUTE2

Jit — Thu, 27 Oct 2016 11:21:44 -0500

IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes. Most people use just a couple of the program's basic functions, but we have also built up a collection of specialized and powerful options. If you are new to IMPUTE2, or indeed to phasing and imputation in general, we suggest that you start by learning the basics.

You should begin by downloading the program from here. You will need to choose the link that matches your computing platform and then follow the instructions for opening the download package.

Once you have done this, you will be ready to try some example analyses on the test data that are provided with the download. The section on Examples shows how to use the most common IMPUTE2 functions. We suggest that you work through these examples and try to understand what the elements of each command are doing. If you don't understand something or would like to know if the program can perform a function that isn't listed, you can read our FAQ or submit a question to our mail list.

When you have learned the basic functionality of the program, you can use several features of this website to prepare your own analysis:

Learn about best practices for imputation.
Download reference data that you can use to impute genotypes in your study.
Look through a complete list of program options.

Address of the bookmark: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html

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

R Graphical Cookbook by Winston Chang

Abhimanyu Singh — Fri, 04 Nov 2016 12:50:30 -0500

R Graphical Cookbook by Winston Chang

A very nice book by Winston Chang for R ethusiast. The R code presented in these pages is the R code actually used to produce the Figures in the book. There will be differences compared to the code chunks shown in the text of the book, but in most cases the differences will be that these pages contain additional code to lay out multiple plots on a single "page".

The code presented for each figure is self-contained, i.e., all code required to produce the figure is included. This means that there is sometimes considerable overlap of code between several figures In some cases, it may be necessary to install an add-on package from CRAN to get the code to run.

More books at http://www.e-reading.club/bookreader.php/137370/C486x_APPb.pdf

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

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

Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation

Neel — Sun, 03 Apr 2022 20:35:19 -0500

Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the read alignment and variant caller’s internal score. Merfin increased the precision of genotyped calls in several benchmarks, improved consensus accuracy and reduced frameshift errors when applied to human and nonhuman assemblies built from Pacific Biosciences HiFi and continuous long reads or Oxford Nanopore reads, including the first complete human genome. Moreover, we introduce assembly quality and completeness metrics that account for the expected genomic copy numbers.

More at https://www.nature.com/articles/s41592-022-01445-y

Address of the bookmark: https://github.com/arangrhie/merfin

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