BOL: Related items

BASE: a practical de novo assembler for large genomes using long NGS reads

Rahul Nayak — Fri, 19 Oct 2018 07:25:21 -0500

new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs.

Address of the bookmark: https://github.com/dhlbh/BASE

Gepard: allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes

Jit — Mon, 26 Aug 2019 11:38:30 -0500

Gepard (German: "cheetah", Backronym for "GEnome PAir - Rapid Dotter") allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes. Reference: Krumsiek J, Arnold R, Rattei T. Gepard: A rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 2007; 23(8): 1026-8. PMID: 17309896

http://cube.univie.ac.at/gepard

Address of the bookmark: https://github.com/univieCUBE/gepard

mutatrix: a population genome simulator which generates simulated genomes.

Jit — Tue, 28 Jan 2020 04:06:58 -0600

genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms

More at https://github.com/ekg/mutatrix

./mutatrix -S sample -P test/ -p 2 -n 10 reference.fasta

Address of the bookmark: https://github.com/ekg/mutatrix

CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes

Jit — Wed, 10 Mar 2021 06:13:49 -0600

The pipeline can use information from scaffolded assemblies (for example from HiC or 10X Genomics), or even from diverged (~65-100 Mya) reference genomes for ordering the contigs and thus support the assembly process. This typically results in improved contig N50 when compared to current state of the art methods.

For smaller vertebrate genomes (~1 Gbp) chromosome scale assemblies can be achieved within 12h on high-end Desktop computers (Intel i7, 12 CPU threads, 128 GB RAM). Larger mammalian genomes (~3Gbp) can be processed within 15-18 h on server equipment (Xeon, 96 CPU threads, 1TB RAM).

Address of the bookmark: https://github.com/HMPNK/CSA2.6

IRscope: an online program to visualize the junction sites of chloroplast genomes

Neel — Wed, 25 Nov 2020 19:44:46 -0600

eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust inferences.

Address of the bookmark: https://sites.google.com/g.hmc.edu/empress/home

Proksee: in-depth characterization and visualization of bacterial genomes

LEGE — Tue, 09 May 2023 19:38:52 -0500

Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file.

Address of the bookmark: https://proksee.ca/

TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes

LEGE — Fri, 14 Feb 2025 10:53:48 -0600

This is the documentation of TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes. It was developed in the research group Domestication Genomics at the Leibniz Institute of Plant Genetics and Crop Research (IPK) Gatersleben.

Address of the bookmark: https://tritexassembly.bitbucket.io/

Sr. Scientist Bioinformatics Vacancies at Indian Institute of Toxicology Research, India

Tue, 01 Sep 2020 07:21:04 -0500

Start date of online Registration: Wednesday August 19, 2020 11:00 Hrs IST
Last date for Registration: Monday September 21, 2020 17:30 Hrs IST
Last date for submission of online application: Monday September 21, 2020 17:30 Hrs IST
Last date of Receipt of physical copy of application at CSIR-IITR: Tuesday October 05, 2020 17:30 Hrs IST

Pay Matrix Level-12
No. of Post-01
(UR)
Post – Sr. Scientist
Area Bioinformatics
Age limit : 37 years
PhD in Computational Biology/Bioinformatics with 2 years experience in desired area
Or
ME/M.Tech in Bioinformatics or Genome Informatics or Genetic Engineering with 3 years experience in desired area
Experience of understanding fundamental science behind Artificial Intelligence, machine learning, novel Artificial Intelligence algorithms and architectures, software engineering principles for Artificial Intelligence, natural language processing with proficiency in programming as evident by publications in SCI journals with high impact factor. To be part a group of scientists working in the area of genomics, running the central
bioinformatics facility, developing independent projects and providing bioinformatics support to the user scientists of the Institute.

More at

http://14.139.62.50/CSIR-IITR%20Scientist%20Recruitment%20Adv%202020.pdf

Genome Annotation

Sun, 25 Aug 2013 10:53:01 -0500

Dr. Rob Edwards describes some of the problems, challenges, and approches in genome annotation, with a particular emphasis on how the Fellowship for the Interpretation of Genomes (FIG) developed subsystems using the SEED database available at http://www.theseed.org/

Pollux: platform independent error correction of single and mixed genomes

Jit — Fri, 19 May 2017 09:41:27 -0500

Pollux: General-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and correct insertion, deletion, and homopolymer errors while remaining sensitive to low coverage areas of sequencing projects. Using published data sets, we correct 94% of Illumina MiSeq errors, 88% of Ion Torrent PGM errors, 85% of Roche 454 GS Junior errors. Introduced errors are 20 to 70 times more rare than successfully corrected errors. Furthermore, we show that the quality of assemblies improves when reads are corrected by our software.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0435-6

Address of the bookmark: https://github.com/emarinier/pollux