BOL: Related items

MGcV: the microbial genomic context viewer for comparative genome analysis

Jit — Mon, 29 Jan 2018 04:55:46 -0600

MGcV is an interactive web-based visalization tool tailored to facilitate small scale genome analysis. To start using MGcV:

Supply your genes/genomic segments/phylogenetic tree of interest in the input-box by
- selecting the type of identifier and pasting identifiers (one per line)
- or by using the gene ID search tool
- or with the BLAST search tool
Click "Visualize context".

Consult the documentation to learn more about MGcV.

Address of the bookmark: http://mgcv.cmbi.ru.nl/

SciLifeLab tutorial for bioinformatics analysis !

Jit — Tue, 17 Apr 2018 04:33:00 -0500

SciLifeLab is a national center for molecular biosciences with focus on health and environmental research.

Courses

Old courses (2012-2014)

pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction

LEGE — Wed, 21 Feb 2024 06:19:41 -0600

ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

Address of the bookmark: https://github.com/AusARG/pipesnake

Bioinformatics Training Courses At RASA LSI

RASA Life Sciences — Wed, 06 Nov 2019 00:30:51 -0600

RASA conducts comprehensive Life Science skill development training courses in Pune, India for working professionals, researchers, students and job-seeker. The trainings are crafted meticulously, covering different modules of courses such as Bioinformatics course, In silico Drug Discovery course, Next Generation Sequence data analysis course, Molecular Biology & Life science software development course wherein you learn from industry leaders how to apply these skills in life science & have a command over software developing process by using various methodologies. We conduct in-class training and instructor-led live online classes worldwide, along with corporate and skill development training worldwide.

Workshops are conducted in regular intervals on Drug Designing, Protein Modeling and Simulation, Chemoinformatics, Bioinformatics etc.The workshops are highly beneficial for working professionals, students, researcher for enhancements of the skills in short duration.

Centurion

Jit — Fri, 12 Feb 2016 04:45:41 -0600

Although centromeres are essential for life and are the subject of extensive research, centromere locations in yeast genomes are difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation assay Hi-C has been re-purposed for diverse applications, including de novo genome assembly, deconvolution of metagenomic samples, and inference of centromere locations. We describe a method, Centurion, that jointly infers the locations of all centromeres in a single yeast genome by exploiting the centromeres’ tendency to cluster in 3D space. We first demonstrate the accuracy of Centurion in identifying known centromere locations from high coverage Hi-C data of budding yeast and a human malaria parasite. We then use two metagenomic samples with relatively low coverage Hi-C data to infer centromere locations for each chromosome in 14 different yeast species. For yeasts with large centromeres (e.g., S. pombe) Centurion predicts the exact centromere locations. For seven yeasts with point centromeres, Centurion predicts most of the centromeres at an average of 5~kb distance from their known locations. Finally, we predict centromere coordinates for six yeast species that currently lack centromere annotations. These results suggest that Centurion can be used for centromere identification for a large number of yeast species, even with a limited amount of Hi-C sequencing.

Paper:http://www.ncbi.nlm.nih.gov/pubmed/25940625

More at http://cbio.ensmp.fr/centurion/

Address of the bookmark: http://cbio.ensmp.fr/centurion/

MITOS: improved de novo metazoan mitochondrial genome annotation

Jit — Fri, 26 Oct 2018 08:25:39 -0500

Allows automatic annotation of metazoan mitochondrial genomes. MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. The software allows for a systematic error screening, the standardisation of gene name and gene boundary designation, anticodon labelling of tRNAs, and provides the means for the assessment of the validity of a gene assignment.

Address of the bookmark: http://mitos.bioinf.uni-leipzig.de/index.py

multiPhATE: bioinformatics pipeline for functional annotation of phage isolates

Abhimanyu Singh — Thu, 16 May 2019 00:17:39 -0500

multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene-calling algorithm and assigns putative functions to gene calls using protein-, virus-, and phage-centric databases.

Address of the bookmark: https://github.com/carolzhou/multiPhATE

Useful Bioinformatics Analysis Tools !

Neel — Thu, 23 Dec 2021 23:10:02 -0600

CoMeta

Classificier of reads from metagenomic sequencing experiments.

• Kawulok, J., Deorowicz, S., CoMeta: Classification of Metagenomes Using k-mers, PLOS ONE, 2015; 10(4):1–23,

CoMSA

Compressor of multiple sequence alignments of proteins.

• Deorowicz, S., Walczyszyn, J., Debudaj-Grabysz, A., CoMSA: compression of protein multiple sequence alignment files, Bioinformatics, 2019; 35(2):22–234,

DSRC

Compressor of sequencing reads.

• Roguski, L., Deorowicz, S., DSRC 2: Industry-oriented compression of FASTQ files, Bioinformatics, 2014; 30(15):2213–2215,
• Deorowicz, S., Grabowski, Sz., Compression of DNA sequences in FASTQ format, Bioinformatics, 2011; 27(6):860–862,

FAMSA

Multiple sequence alignment designed for huge families of proteins (even containing hundreds of thousands of sequences).

• Deorowicz, S., Debudaj-Grabysz, A., Gudys, A., FAMSA: Fast and accurate multiple sequence alignment of huge protein families, Scientific Reports, 2016; 6(33964):

FaStore

Compressor of FASTQ files.

• Roguski, L., Ochoa, I., Hernaez, M., Deorowicz, S., FaStore - a space-saving solution for raw sequencing data, Bioinformatics, 2018; 34(16):2748–2756,

FQSqueezer

Experimental high-end compressor of FASTQ files.

• Deorowicz, S., FQSqueezer: k-mer-based compression of sequencing data, Scientific Reports, 2020; 10(578):

GDC

Compressor of collections of genome sequences.

• Deorowicz, S., Danek, A., Niemiec, M., GDC 2: Compression of large collections of genomes, Scientific Reports, 2015; 5(11565):1–12,
• Deorowicz, S., Grabowski, Sz., Robust relative compression of genomes with random access, Bioinformatics, 2011; 27(21):2979–2986,

GTC

Genotype databases compressor with support for fast queries.

• Danek, A., Deorowicz, S., GTC: how to maintain huge genotype collections in a compressed form, Bioinformatics, 2018; 34(11):1834–1840,

GTShark

Genotypes compressor.

• Deorowicz, S., Danek, A., GTShark: Genotype compression in large projects, Bioinformatics, 2019; 35(22):4791–4793,

KMC

Memory frugal k-mer counter.

•  Kokot, M., Długosz, M., Deorowicz, S., KMC 3: counting and manipulating k -mer statistics, Bioinformatics, 2017; 33(17):2759–2761,
•  Deorowicz, S., Kokot, M., Grabowski, Sz., Debudaj-Grabysz, A., KMC 2: Fast and resource-frugal k-mer counting, Bioinformatics, 2015; 31(10):1569–1576,
•  Deorowicz, S., Debudaj-Grabysz, A., Grabowski, Sz., Disk-based k-mer counting on a PC, BMC Bioinformatics, 2013; 14():Article no. 160,

Kmer-db

Tool for estimation of evolutionary distances in a collection of genomes.

• Deorowicz, S., Gudys, A., Dlugosz, M., Kokot, M., Danek, A., Kmer-db: instant evolutionary distance estimation, Bioinformatics, 2019; 35(1):133–136,

MuGI

Index allowing queries for a collection of multiple genome sequences.

• Danek, A., Deorowicz, S., Grabowski, Sz., Indexes of Large Genome Collections on a PC, PLOS ONE, 2014; 9(10):e109384,

ORCOM

Experimental compressor of sequencing reads.

• Grabowski, Sz., Deorowicz, S., Roguski, L., Disk-based compression of data from genome sequencing, Bioinformatics, 2014; 31(9):1389–1395,

PgSA

Index allowing queries for a collection of sequencing reads.

• Kowalski, T., Grabowski, Sz., Deorowicz, S., Indexing arbitrary-length k-mers in sequencing reads, PLOS ONE, 2015; 10(7):1–16,

QuickProbs

Multiple sequence alignment designed especially for GPU.

• Gudys, A., Deorowicz, S., QuickProbs 2: towards rapid construction of high-quality alignments of large protein families, Scientific Reports, 2017; 7(41553):
• Gudys, A., Deorowicz, S., QuickProbs – A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors, PLOS ONE, 2014; 9(2):e88901,

RECKONER

Read error corrector.

• Maciej Długosz, M., Deorowicz, S., RECKONER: read error corrector based on KMC, Bioinformatics, 2017; 33(7):1086–1089,

TGC

Compressor of collections of genomes given in Variant Call Format (VCF) files.

• Deorowicz, S., Danek, A., Grabowski, Sz., Genome compression: a novel approach for large collections, Bioinformatics, 2013; 29(20):2572–2578,

VCFShark

Compressor of VCF files.

• Deorowicz, S., Danek, A., GTShark: Genotype compression in large projects, biorxiv.org, 2020; ():

Whisper

Experimental mapper of whole genome sequencing data.

•  Deorowicz, S., Gudys, A., Whisper 2: indel-sensitive short read mapping, bioRxiv.org, 2019; :
•  Deorowicz, S., Debudaj-Grabysz, A., Gudys, A., Grabowski, Sz., Whisper: read sorting allows robust robust mapping of DNA sequencing data, Bioinformatics, 2019; 35(12):2043–2050,
•  Deorowicz, S., Debudaj-Grabysz, A., Gudys, A., Grabowski, Sz., Robust mapping of whole genome sequencing data, Poster at The Biology of Genomes Conference, 2017;

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

Neel — Tue, 30 Nov 2021 23:23:57 -0600

MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads.

https://academic.oup.com/nar/article/47/11/e63/5377471

Address of the bookmark: https://github.com/linzhi2013/MitoZ

NGS course Medical Genomics, scheduled for 17-20 September 2013 in UZ Leuven (Belgium).

Poonam Mahapatra — Mon, 12 Aug 2013 12:08:24 -0500

This course is open to all students and postdocs and registration for all academic participants is free of charge. To help us in organizing the course, please register online via http://gc.uzleuven.be where the preliminary program is also available.

This course is organized with support from the IAP “Belgian Medical Genomics Initiative”, SymBioSys and the Genomics Core.

For inquiries, please email Ms Narcisse Opdekamp ( narcisse.opdekamp@uzleuven.be ).

More at >> http://gc.uzleuven.be/

BOL: Related items

MGcV: the microbial genomic context viewer for comparative genome analysis

SciLifeLab tutorial for bioinformatics analysis !

Courses

Metagenomics Workshop

Introduction to Bioinformatics Using NGS Data

Introduction to Genome Annotation

De Novo Genome Assembly

RNA-seq course

R Programming Foundations for Life Scientists

Single cell RNA sequencing analysis