BOL: Related items

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

Anjana — Tue, 10 May 2016 07:46:24 -0500

High-throughput genomics has revolutionized biological research, however, while the number of sequenced genomes grows by the day, quality assessment of the resulting assembled sequences remains complicated and mostly limited to technical measures like N50.
BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
BUSCO assessments are implemented in open-source software, with comprehensive lineage-specific sets of Benchmarking Universal Single-Copy Orthologs for arthropods, vertebrates, metazoans, fungi, eukaryotes, and bacteria.
These conserved orthologs are ideal candidates for large-scale phylogenomics studies, and the annotated BUSCO gene models built during genome assessments provide a comprehensive gene predictor training set for use as part of genome annotation pipelines.
BUSCO assessments offer intuitive metrics, based on evolutionarily informed expectations of gene content from hundreds of species, to gauge completeness of rapidly accumulating genomic data and satisfy an Iberian's quest for quality - "Busco calidad/qualidade".

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

Blobology

Jit — Mon, 13 Jun 2016 10:18:33 -0500

Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step

Blaxter Lab, Institute of Evolutionary Biology, University of Edinburgh

Goal: To create blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step.

This repository accompanies the paper:
Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots. Sujai Kumar, Martin Jones, Georgios Koutsovoulos, Michael Clarke, Mark Blaxter
(submitted 2013-10-01 to Frontiers in Bioinformatics and Computational Biology special issue : Quality assessment and control of high-throughput sequencing data).

It contains bash/perl/R scripts for running the analysis presented in the paper to create a preliminary assembly, and to create and collate GC content, read coverage and taxon annotation for the preliminary assembly, which can be visualised, such as Figure 2a from the paper showing TAGC plots/blobplots for Caenorhabditis sp. 5:

Address of the bookmark: https://github.com/blaxterlab/blobology

HGA

Jit — Tue, 29 Nov 2016 07:25:53 -0600

HGA tool version 1.0 This tool helps to apply the Hierarchical Genome Assembly (HGA) method. The tool will apply: 1. Partitioning a given reads dataset into a given number of partitions. 2. Assembling each partitions using a pre-specified assembler (Velvet or SPAdes in this version) and using a given kmer size. 3. Merging all the assemblies of the partition. 4. Combining all the assemblies of the partition (using velvet with kmer value of 31). 5. Finaly, re-assembling the whole dataset with the merged contigs or the combined contigs, using a given kmer size.

https://github.com/aalokaily/Hierarchical-Genome-Assembly-HGA

Address of the bookmark: https://github.com/aalokaily/Hierarchical-Genome-Assembly-HGA

Assembly Course

Shruti Paniwala — Mon, 10 Jul 2017 09:38:05 -0500

https://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture6.pdf

Address of the bookmark: https://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture6.pdf

BEAP: Blast Extension and Assembly Program

Shruti Paniwala — Mon, 11 Jun 2018 04:52:56 -0500

The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the "primer" therefore help to "extend" the length of the original sequence for constructing a "full length" sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference. https://www.animalgenome.org/tools/beap/

Address of the bookmark: https://www.animalgenome.org/tools/beap/

lsugenomics Lab

Thu, 07 Jul 2022 05:26:37 -0500

In our lab, we seek to characterize and to compare genomes in order to better understand genetic and evolutionary processes linking genotypes to phenotypes.

Sequencing and decoding plant genomes have been integral in our approaches.

The overarching goal of our research is to understand how to interpret complex and fascinating messages embedded in genomes.

https://www.lsugenomics.org/

Tigers genome sequenced

Rahul Agarwal — Tue, 17 Sep 2013 16:48:24 -0500

Fifteen scientists led by Dr Jong Bhak of Genome Research Foundation, South Korea, decoded as many as 3 billion nucleotides (organic molecules that form the basic building blocks of nucleic acids, such as DNA). They identified 20,000 genes related to various functions of the tiger.

The biggest and perhaps most fearsome of the world's big cats, the tiger, shares 95.6 percent of its DNA with humans' cute and furry companions, domestic cats.

The new research showed that big cats have genetic mutations that enabled them to be carnivores. The team also identified mutations that allow snow leopards to thrive at high altitudes.

Reference:

http://www.nbcnews.com/science/your-cat-ferocious-tigers-share-lot-95-6-percent-their-4B11182690

http://timesofindia.indiatimes.com/home/environment/flora-fauna/Gene-mapping-of-tiger-completed/articleshow/22671681.cms

Paper:

http://www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html

Opera: An optimal genome scaffolding program

Jit — Mon, 27 Nov 2017 10:18:20 -0600

Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads.

An updated version called OPERA-LG has been re-engineered with features for the assembly of large and complex genomes.

Song Gao, Denis Bertrand, Burton K. H. Chia and Niranjan Nagarajan. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees. Genome Biology, May 2016, doi: 10.1186/s13059-016-0951-y.

Song Gao, Wing-Kin Sung, Niranjan Nagarajan. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. Journal of Computational Biology, Sept. 2011, doi:10.1089/cmb.2011.0170.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0951-y

Address of the bookmark: https://sourceforge.net/projects/operasf/

Scripts for the analysis of HGT in genome sequence data.

Jit — Wed, 29 Nov 2017 16:44:10 -0600

Scripts for the analysis of HGT in genome sequence data

Address of the bookmark: https://github.com/reubwn/hgt

Mugsy: multiple whole genome alignment tool

Jit — Fri, 08 Dec 2017 17:41:14 -0600

Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.

To cite Mugsy, use:

Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes.Bioinformatics 2011 27(3):334-4

Address of the bookmark: http://mugsy.sourceforge.net/