BOL: Related items

Genome Origami

Jitendra Narayan — Fri, 12 Dec 2014 22:48:17 -0600

There are several interesting factoid about our genomes, one of them is their folding. If we stretched out the DNA in a single cell, which is only a few millionths of an inch wide, it would span more than six feet. In other word, the size of six feet DNA fold themself to fit in a few millionths of an inch wide space. These DNA folding is a dynamic process that changes over time (!!). Researchers around the world have been trying to understand how DNA folds itself up so efficiently, and a recent post on the NIH Director’s Blog highlights new research illustrating how the human genome folds inside the cell’s nucleus, as well as how DNA folding affects gene regulation. The research team created this delightful video that demonstrates the principles involved using origami art.

http://bioinformaticsonline.com/videolist/watch/19555/a-3d-map-of-the-human-genome

Researchers have been working to determine how cells regulate gene expression for nearly as long as we’ve known about DNA. How, for example, do nerve cells know to turn off only nerve cell genes and turn off bone cell genes? DNA folding loops are part of the answer. This research team, which published their findings in a paper in Cell http://www.cell.com/cell/abstract/S0092-8674%2814%2901497-4 , found that the number of loops is much lower than expected. There are only 10,000 loops instead of the predicted millions, and they form on/off switches in DNA.

More at http://www.eurekalert.org/pub_releases/2014-12/ru-3mr121114.php

Reference http://www.cell.com/cell/abstract/S0092-8674%2814%2901497-4

Choosing the Right NGS Sequencing Instrument for Your Study

Neel — Wed, 15 Jun 2022 00:37:29 -0500

The right sequencing instrument for your study depends on your project goal. Setting aside turnaround time and price, it essentially comes down to the numbers of reads and read length you need for your experiment. Below, we've described and compared metrics for each of the instruments available. If you’re new to high-throughput sequencing and have questions about how you should design your sequencing run, fill out our free consultation form and we'll get in touch with you to help.

More at https://genohub.com/ngs-instrument-guide/

Address of the bookmark: https://genohub.com/ngs-instrument-guide/

WALK – IN – INTERVIEW @ Agricultural Knowledge Management Unit Indian Agricultural Research Institute, New Delhi-110012

Fri, 12 Dec 2014 21:33:02 -0600

Walk-in-interview for the following temporary positions will be conducted on 20th December 2014 (between 10:00 AM to 01:00 PM) at Agricultural Knowledge Management Unit, A0 block (Ground Floor), LBS Building, Indian Agricultural Research Institute, New Delhi-110012:

1 Dr. A.K.Mishra Coordinator & PI (BTISnet)

Traineeship (two) for one year

Rs. 5000/- (consolidated)

M.Sc. (Bioinformatics) with 60 % marks from a recognized University

20-12-2014 (10:00 AM -11:00 AM)

Studentship (four) for one year

Rs. 2500/- (consolidated)

Final year M.Sc./ M.Tech (Bioinformatics) Students from a recognized University

20-12-2014 (11:00 AM- 1:00 PM)

The positions are purely temporary and co-terminus with the DBT Programme. Eligible candidates are requested to submit the application form in the prescribed format along with original certificates/ documents (Degree, Marks sheets, Work experience, if any) at the time of interview. No TA/DA will be paid. Maximum age limit is 28 years for all positions. Age relaxation of 5 yrs for SC/ST and woman candidates and 3 years for OBC candidates will be given. Canvassing in any form invites disqualification.

Advertisement: http://www.iari.res.in/files/BIC-08122014-20141208-172344.pdf

Libraries or management tools for high throughput sequencing data

LEGE — Fri, 04 Oct 2024 02:45:06 -0500

GATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.
These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). Among them are (the full is available here: https://gatb.inria.fr/software/):
LRez: C++ Library and toolkit for the barcode-based management and indexation of linked-read datasets.

Variant calling and/or genotyping

DiscoSNP++ and discoSnpRAD: Reference-free small variant discovery (SNPs and indels)
MindTheGap: Detection and assembly of large insertion variants
TakeABreak: reference-free inversion discovery tool
SVJedi: Structural Variant genotyper with long read data
SVJedi-graph: Structural Variant genotyper with long read data using a variation graph

Sequence assembly

MinYS: reference-guided genome assembly in metagenomics data
MTG-link: local assembly tool for linked-read data
Minia: De novo short read assembler
de-novo pipeline: de-novo assembly pipeline (error correction / contigs / scaffolding) for genomes and meta-genomes
Mapsembler2: Targeted assembly (not maintained)

Managing k-mers & indexation

findere: simple strategy for speeding up queries and for reducing false positive calls from any Approximate Membership Query data structure.
- fimpera extends findere adding the abundance information.
kmtricks: modular tool suite for counting kmers, and constructing Bloom filters or kmer matrices, for large collections of sequencing data.
kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks.
back to sequences: Find sequences (reads, unitigs, genes) related to a set of kmers in large datasets, in a matter of seconds.
Backpack Quotient Filter: k-mer indexing data structure with abundance
short read connector: Detect similar reads from potentially large read set
DSK: Count K-mer in sequences

Pangenome graph manipulation

Pancat: Pangenome Comparison and Analysis Toolkit
GFAGraphs: a Python library to handle pangenome graph files in GFA format.

Comparative metagenomics with k-mers

Simka and SimkaMin: Comparative metagenomics for large-scale datasets
Comparead & Commet: comparison of metagenomic datasets

Species and bacterial strains identification

ORI: software using long nanopore reads to identify bacteria present in a sample at the strain level
StrainFLAIR: STRAIN-level proFiLing using vArIation gRaph

General-purpose sequencing data manipulation

GASSST: long read mapper
Leon: short read compressor (now included in GATB-core)
Bloocoo: short read corrector
BCALM: Construct compacted de Bruijn graphs (unitigs)

Protein Structure

A_Purva: Contact Map Overlap solver
MD-Jeep: Distance Geometry solver
CSA: Comparative Structural Alignment

Workflow

SLICEE: parallel execution of bioinformatics workflows

Comparative Genomics

CASSIS: detection of rearrangement breakpoints
PLAST: intensive bank-to-bank sequence comparison
DRJBreakpointFinder: detection and precise localization of excision sites in proviral segments

My commonly used commands in Bioinformatics

Rahul Nayak — Thu, 26 Jul 2018 04:58:45 -0500

FYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually:

minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta racon_assembly.fasta
nucmer -p nucmer assembly.fasta racon_assembly.fasta
show-snps -C -T -r nucmer.delta

This reports Racon's changes in a table. You can exclude indels with the -I option in show-snps.

This process (Racon -> MUMmer -> SNP table) solves the problem I originally raised in this issue. So as far as I'm concerned, you can close this issue (or keep it open if you still want to implement some kind of variant table).

Studentship at Nagaland University

Tue, 16 Dec 2014 01:35:00 -0600

Nagaland University
(A Central University Estd. By the Act of Parliament No. 35 of 1989)
Lumami 798 627, Nagaland
DBT Sponsored ‘Bioinformatics Infrastructure Facility’ Centre

Applications in plain paper are invited for the posts of (1) Traineeship (2 Nos.) and (2) Studentship – (2 Nos.) in the DBT funded-Bioinformatics Infrastructure Facility (BIF), Nagaland University, Lumami-798627, Nagaland. Details are given below. Interested candidates may submit the application along with self attested copies of certificates in support of the candidature to Prof. Chitta Ranjan Deb, Coordinator or Dr. L. N. Kakati, Deputy Coordinator, BIF Centre, Nagaland University, Lumami-798627, Nagaland on or before 15th January 2015.

The scanned application with relevant documents may be sent by email attachment to bifnulumami@gmail.com. Shortlisted candidates will be informed by email if called for interview. No TA/DA is admissible for attending the interview.

Traineeship (Two nos.)

Post Graduate degree in any branch of Life Sciences from UGC recognized Universities

Knowledge of computers and bioinformatics

Rs.8000/- p.m. fixed.

6 months

Studentship (Two nos.)

Pursuing Post Graduate degree in any branch of Life Sciences from UGC recognized Universities

Knowledge of computers and bioinformatics

Rs.8000/- p.m. fixed.

6 months

Terms and Conditions:

i) Applicants need to produce all original documents if call for interview.
ii) The posts are purely temporary and the appointment does not confer any entitlement or right over the job and will not be considered as formal service.
iii) No TA & DA will be paid for appearing in the walk-in-interview.
iv) The stipend/salary amount is subject to the sanction of DBT, New Delhi.

Advertisement: http://www.nagauniv.org.in/files/BIF%20Advt.pdf

Referee: Genome assembly quality scores

Jit — Sun, 04 Nov 2018 16:44:30 -0600

Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site in an assembled genome to calculate a quality score for each position in the genome assembly.

We accomplish this by first calculating genotype likelihoods for every site. For a given site in a diploid genome, there are 10 possible genotypes (AA, AC, AG, AT, CC, CG, CT, GG, GT, TT). Referee takes as input the genotype likelihoods calculated for all 10 genotypes given the called reference base at each position.

Referee is a program to calculate a quality score for every position in a genome assembly. This allows for easy filtering of low quality sites for any downstream analysis.

https://github.com/gwct/referee

Address of the bookmark: https://gwct.github.io/referee/#

Senior Scientist (Agricultural Bio-informatics) (One post)

Wed, 24 Dec 2014 05:01:02 -0600

Agricultural Scientists Recruitment Board

Qualifications Essential:
Doctoral degree in Bio-informatics/ Biotechnology/Molecular Biology and Biotechnology/Life Sciences/ Computer Sciences with specialization in Bio-informatics including relevant basic sciences with 8 years’ experience in the relevant subject as Scientist/Lecturer or in an equivalent position in the Pay Band- 3 of 15600-39100 with Grade Pay of 5400/6000/7000/8000 having made contribution to research/teachin/extension education as evidenced by published work/innovations and impact.

Doctoral degree in the above subject(s) including relevant basic sciences with minimum 8 years’ experience of high quality post-doctoral research in an institution/organization as evidenced by at least 6 publications in journals with NAAS rating of 7.5 or above.

Desirable:
(i) Specialization and experience: Knowledge of software development and its application in crop bioinformatics, experience in handling ‘omies’data.
(ii) Teaching experience in relevant subject

The Secretary, Agricultural Scientists Recruitment Board, Indian Council of Agricultural Research Krishi Anusandhan Bhavan-I, Pusa New Delhi –110 012, India

Detailed eligibility criteria with how to apply information can be had at:
http://www.indiastudychannel.com/jobs/333467-Indian-Council-of-Agricultural-Research-looking-for-Assistant-Director-General.aspx

More at http://asrb.org.in/administrator/uploads_dir/1418978057english.pdf

jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator

Abhimanyu Singh — Fri, 26 Jul 2019 00:58:12 -0500

jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. All outputs can be written to standard file formats.

A swift, versatile phylogenomic and high-throughput sequencing simulator https://jackalope.lucasnell.com

Address of the bookmark: https://github.com/lucasnell/jackalope

RStudio

Jitendra Narayan — Sat, 27 Dec 2014 06:50:58 -0600

RStudio IDE is a powerful and productive user interface for R. It’s free and open source, and works great on Windows, Mac, and Linux.

The developers and expert trainers are the authors of several popular R packages, including ggplot2, plyr, lubridate, and others.

More at http://www.rstudio.com/

http://www.rstudio.com/products/RStudio/

Address of the bookmark: http://www.rstudio.com/