BOL: Related items

bpRNA: large-scale automated annotation and analysis of RNA secondary structure

Rahul Nayak — Wed, 23 May 2018 03:24:33 -0500

bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature.

The bpRNA code is written in perl and requires the Graph perl module. Several additional scripts for analysis are included. The source code is available at http://github.com/hendrixlab/bpRNA.

Address of the bookmark: http://github.com/hendrixlab/bpRNA

PANNZER: a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function.

BioStar — Thu, 13 Aug 2020 09:57:24 -0500

PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function.

PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE) and GO classes.

PANNZER2 processes bacterial proteomes in minutes and eukaryotic proteomes in an hour. You can use AAI-profiler to summarize a proteome's species neighbors and reveal taxonomic identity or contamination.

Address of the bookmark: http://ekhidna2.biocenter.helsinki.fi/sanspanz/#

SeqMule: Automated human exome/genome variants detection

BioStar — Tue, 18 Feb 2020 03:22:54 -0600

SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file.

Address of the bookmark: https://doc-openbio.readthedocs.io/projects/seqmule/en/latest/

Metagenomics role in antibiotic resistance

Rahul Agarwal — Mon, 02 Jun 2014 08:04:40 -0500

Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets

Neel — Sat, 06 Jul 2019 13:56:10 -0500

Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them.

Developper: Gaëtan Benoit, PhD, former member of the Genscale team at Inria.

Contact: claire dot lemaitre at inria dot fr

Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets. https://gatb.inria.fr/software/simka/

Address of the bookmark: https://github.com/GATB/simka

ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data

LEGE — Wed, 08 May 2024 07:32:45 -0500

ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate contigs. ContigExtender is effective for extending contigs significantly in in silico synthesized and real metagenomics datasets.

More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953547/

Address of the bookmark: https://github.com/dengzac/contig-extender

Bambus

Jit — Tue, 16 Aug 2016 08:09:15 -0500

Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Home Page:

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus2

Address of the bookmark: https://www.cbcb.umd.edu/software/bambus2

Coordinator of Bioinformatics Core Facility-Robert Koch Institute Berlin

Thu, 30 Jan 2020 07:01:45 -0600

We are offering the following position in unit MF 1 "Bioinformatics" of department MF "Methodology and Research Infrastructure" for a

Coordinator of our Bioinformatics Core Facility (all genders)

(salary dependent on qualifications and experience in accordance with public sector wage scale [TVöD] up to grade E 14).

The contract is not limited. The position will be available immediately.
https://www.researchgate.net/job/938589_Coordinator_of_our_Bioinformatics_Core_Facility_all_genders

Next Generation Sequencing (NGS) Tutorials

Jitendra Narayan — Sat, 24 Aug 2013 06:01:37 -0500

Institute of computational biomedicine, Cornell University provide an NGS workshop tutorial at http://chagall.med.cornell.edu/NGScourse/

You can also add your favourite NGS educational material, or workshop tutorial by commenting on this bookmarks for user benefit.

Understanding the basics of genome sequencing:

Tutorial by Luke Jostins.

http://www.genetic-inference.co.uk/blog/2009/04/basics-sequencing-dna-part-1/

http://www.genetic-inference.co.uk/blog/2009/08/basics-sequencing-dna-part-2/

A window into third-generation sequencing

http://hmg.oxfordjournals.org/content/19/R2/R227.full.pdf

==============================================

NGS data analysis pipelines

Detecting and annotating genetic variations using the HugeSeq pipeline DOI: 10.1038/nbt.2134
NARWHAL, a primary analysis pipeline for NGS data http://bioinformatics.oxfordjournals.org/cgi/content/abstract/28/2/284?etoc
RseqFlow: Workflows for RNA-Seq data analysis DOI: 10.1093/bioinformatics/btr441
ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence 10.1186/1471-2164-12-285
A framework for variation discovery and genotyping using next-generation DNA sequencing data PubMed: 21478889
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects DOI: 10.1186/1471-2105-12-134 Abstract: http://www.biomedcentral.com/1471-2105/12/134/abstract
WEP: a high-performance analysis pipeline for whole-exome data http://www.biomedcentral.com/1471-2105/14/S7/S11
DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data. http://www.ncbi.nlm.nih.gov/pubmed/23657089
GATK: a Toolkit for Genome Analysis http://www.broadinstitute.org/gatk/
Metagenomics:http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsmetagenomics/
RNASeq:http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsrnaseq/
Bioinformatics and Seq courses: http://www.isb-sib.ch/training/training-activities-schedule/archive-2013.html
Variant Detection (Model organism) Advanced tutorial https://docs.google.com/document/pub?id=1CuKkKylVDb03tnN7RSWl5EUzleetn0ctjmvaidPKLxM
Variant Detection Introductory tutorial https://docs.google.com/document/pub?id=1ZRzrjjOCvtAu3m-IKL-rbJ1f4On60dDL_IEwG7oejdI
Microbial de novo Assembly for Illumina Data Introductory tutorial https://docs.google.com/document/pub?id=1N3AB9ptISUu4zULqe1kXpVF0BDyGb5f5yzxWSJd_WNM
RNAseq Differential Gene Expression Introductory tutorial https://docs.google.com/document/pub?id=1KbTiBHtvHLfPRZ39AY3uriazrINA8TJzgjjwn1zPP7Y

" Please add your favourite NGS link below in comment section for the benefit of bioinformatics community ".

Address of the bookmark: http://chagall.med.cornell.edu/NGScourse/

BUSCO

Jitendra Narayan — Sun, 07 Feb 2016 16:02:39 -0600

Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

More at http://busco.ezlab.org/

Address of the bookmark: http://busco.ezlab.org/