BOL: Related items

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

Jit — Tue, 07 Nov 2017 04:36:10 -0600

We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and in scaffolds longer than 269 kilobases. Incorporating fosmid ends recovers entire chromosomes. Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset, avoiding an explicit error correction step as used in other short-read assemblers. A novel memory-efficient hashing scheme is introduced. The resulting contigs are ordered and oriented using paired reads separated by ∼280 bp or ∼3.2 kbp, and many gaps between contigs can be closed using paired-end placements. Practical issues with the dataset are described, and prospects for assembling larger genomes are discussed.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158087/

funannotate: Eukaryotic Genome Annotation Pipeline

Jit — Wed, 19 Sep 2018 07:47:22 -0500

Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this software package was to be able to accurately and easily annotate a genome for submission to NCBI GenBank. Existing tools (such as Maker) require significant manually editing to comply with GenBank submission rules, thus funannotate is aimed at simplifying the genome submission process.

Address of the bookmark: https://github.com/nextgenusfs/funannotate

Earth BioGenome Project

Jit — Wed, 25 Apr 2018 07:48:56 -0500

The central goal of the Earth BioGenome Project is to understand the evolution and organization of life on our planet by sequencing and functionally annotating the genomes of 1.5 million known species of eukaryotes, a massive group that includes plants, animals, fungi and other organisms whose cells have a nucleus that houses their chromosomal DNA. To date, the genomes of less than 0.2 percent of eukaryotic species have been sequenced.

More at https://www.ucdavis.edu/news/earth-biogenome-project-aims-sequence-dna-all-complex-life

SALSA: A tool to scaffold long read assemblies with Hi-C

Jit — Fri, 15 Jun 2018 04:01:15 -0500

This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version, first run the following commands: cd SALSA make To run the code, you will need Python 2.7, BOOST libraries and Networkx(version lower than 1.2). If you consider using this tool, please cite our publication which describes the methods used for scaffolding. Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range contact information. BMC genomics, 18(1), 527. Link Ghurye, J., Rhie, A., Walenz, B.P., Schmitt, A., Selvaraj, S., Pop, M., Phillippy, A.M. and Koren, S., 2018. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. bioRxiv, p.261149 Link For any queries, please either ask on github issue page or send an email to Jay Ghurye (jayg@cs.umd.edu).

Address of the bookmark: https://github.com/machinegun/SALSA

Opening for RA/extended SRF in Bioinformatics project by DBT at Bose Institute

Sun, 01 Mar 2015 00:50:18 -0600

The institute has evolved over the years into a multi-disciplinary research organization with stress on fundamental research in its pursuit of advancement of knowledge in Science and technology and at the same time developing highly competent and able scientific manpower for the country. The institute has on its staff highly qualified and experienced scientists working in the field of Biological, biochemical, Chemical and Physical sciences placed in long established departments of Physics, Chemistry, Botany, Microbiology, Biochemistry, and Biophysics, and the research sections on plant Molecular & Cellular Genetics, Animal Physiology, Immunotechnology and Environmental science

Walk-in-Interview will be held on 04th March 2015 at 11.30 A.M. in the Bio- Informatics Centre of Bose Institute, P-1/12, C.I.T. Scheme VII-M, Kolkata- 700054 for two (02) positions of Research Associate/ Extended Senior Research Fellow in the DBT sponsored following two projects running under the CoE- Bioinformatics under the guidance of Prof. Pinakpani Chakrabarti, Bioinformatics Centre.

Position : RA/SRF
Project title : 1. "Centre of Excellence (CoE) in Bioinformatics at Bose Institute”,2. Project entitled “Setting up of National Facility on Interactive Graphysics Computer System (IGCS) for Biomolecular Modeling, Molecular Dynamics & Structures”

Desired Profile : Ph.D degree in Biological or Chemical Sciences with in-depth understanding of protein structure and dynamics for R.A. position.Those who have submitted thesis can be considered for Extended SRF position
Preferred : Knowledge of computer programming and bioinformatics softwares.
Stipend : For R.A- Rs. 22,000/- p.m., plus admissible H.R.A. and Medical benefit. For Extended SRF - Rs. 20,000/- p.m., plus admissible H.R.A.and Medical benefit.
Age : For R.A- Below 35 years; For Extended SRF - Below 33 years
Interested and eligible candidates should appear before the Selection Committee with atyped application addressed to the Sr.Prof. & In-Charge, Registrar's Office, Bose Institute, P- 1/12, CIT Scheme VII-M, Kankurgachi, Kolkata-700054 along with Bio-data giving details of qualification i.e. examination passed, year, division, percentage of marks from Secondary onwards with attested copies of Certificates, Mark-Sheet and testimonials. The candidates should also bring the original mark-sheets, certificates etc. at the time of Interview.

Walk in Interview : 04.03.15

More at http://www.boseinst.ernet.in/ADVT/14/p_34.pdf

Research Associate Biotechnology/JRF/Lab. Assistant Indian Institute of Vegetable Research (IIVR) - Varanasi, Uttar Pradesh

Wed, 11 Mar 2015 08:59:27 -0500

F. No.: 2-19/2011-Adm.I

Research Associate Biotechnology /JRF / Lab. Assistant recruitment in Indian Institute of Vegetable Research

Project:
Genomics assisted selection of Solanum chilense introgression lines for enhancing drought tolerance in tomato
Post Name : Research Associate
Qualification : Ph.D in Biotechnology/ Bioinformatics/Genetics & Plant Breeding. M. Tech in Computer Science with at least one research paper in science citation indexed journal. Desirable: Experience in bioinformatics and next generation sequence data handling. Familiarity in Linux, R, Perl/Phython or other programming languages. Willingness to travel to European partner centers.

Pay Scale : Rs. 36000 for 1st and 2nd year as per rules for Research Associate. Rs. 25000/- for 1st and 2nd year and Rs. 28000 as per rules for Junior Research Fellow. Rs. 7000/- for Lab. Assistant.

Age : Not more than 35 years for Men and 40 years for Women (Relaxable for SC/ST/OBC/PH candidates as per rules) for Research Associate/ Junior Research Fellow. Minimum age will be 21 years and maximum age will be 45 years (Relaxable for SC/ST/OBC/PH candidates as per rules) for Lab.Assistant.

More at http://iivr.org.in/Job%20Oppurtunities/RA20.03.2015.pdf

Genome sequence-based (sub-)species delineation.

Abhimanyu Singh — Wed, 12 Dec 2018 08:31:14 -0600

The GGDC web service reports digital DDH for a universal and accurate delineation of prokaryotic (sub-)species without inheriting the pitfalls of classic DDH, and also calculates differences in genomic G+C content.

http://ggdc.dsmz.de/ggdc_background.php#

Genome-to-Genome Distance Calculator 2.1

http://ggdc.dsmz.de/ggdc.php

Address of the bookmark: http://ggdc.dsmz.de/

Roary: the Pan Genome Pipeline

Jit — Tue, 22 Jan 2019 05:52:07 -0600

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes.

Address of the bookmark: https://sanger-pathogens.github.io/Roary/

RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs

BioJoker — Wed, 17 Apr 2019 19:45:22 -0500

Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019.

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
Intact ordering and orienting of contigs.
Chimeric contig correction
GFF lift-over
Structural variant calling with and integrated version of Assemblytics
Confidence scores associated with the grouping, localization, and orientation for each contig.

Address of the bookmark: https://github.com/malonge/RaGOO

MGSE: Mapping-based Genome Size Estimation

Shruti Paniwala — Fri, 17 Jan 2020 02:11:43 -0600

MGSE can harness the power of files generated in genome sequencing projects to predict the genome size. Required are the FASTA file containing a high continuity assembly and a BAM file with all available reads mapped to this assembly. The script construct_cov_file.py (https://doi.org/10.1186/s12864-018-5360-z) allows the generation of a COV file based on the (sorted) BAM file (also possible via MGSE directly). Next, this COV file can be used by MGSE to calculate the coverage in provided reference regions and to calculate the total number of mapped bases. Both values are subjected to the genome size estimation. Providing accurate reference regions is crucial for this genome size estimation.

Address of the bookmark: https://github.com/bpucker/MGSE