BOL: Related items

dnaPipeTE: a pipeline designed to find, annotate and quantify Transposable Elements

Jit — Mon, 12 Aug 2019 21:56:08 -0500

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

https://github.com/clemgoub/dnaPipeTE/wiki/dnaPipeTE-WIKI-home

Address of the bookmark: https://github.com/clemgoub/dnaPipeTE

Scalpel

Shruti Paniwala — Wed, 20 Aug 2014 02:07:58 -0500

A team from Cold Spring Harbor Laboratory has released an algorithm, called Scalpel, for finding insertions and deletions in next generation sequencing data sets. Scalpel, which is open source and available for download on SourceForge, outperformed the popular tools GATK HaplotypeCaller and SOAPindel in test runs on both simulated and real whole human exomes.

Like other indel callers, Scalpel works by performing de novo assembly of regions of interest, so that misalignment to the reference genome cannot obscure the presence of an insertion or deletion. Scalpel's innovation is to repeatedly check its assembly before comparing to the reference genome, to account for simple sequence repeats that are a regular source of error in indel calling. When Scalpel assembles an exon, it collects reads that map to that exon (including partial matches), splits them into k-mers, and creates a de Bruijn graph to span the exon; however, if it detects repeats in the map, it iteratively increases the size of the k-mers by one base until the repeats are eliminated. This ensures that the final assembly of the exon is highly accurate while minimizing compute time.

The Cold Spring Harbor team's validation of Scalpel, published over the weekend in Nature Methods, compares Scalpel's performance on a live whole exome against HaplotypeCaller and SOAPindel. The donor is an individual with serious neurological disorders, which may be linked to a high incidence of indels. One thousand indels from this individual's exome, called by one or more of the informatics pipelines, were selected for focused resequencing. This resequencing revealed a 77% true positive rate for Scalpel calls, dramatically better than the rates for either of the competing tools; Scalpel performed especially well with indels longer than five base pairs, a traditional weak point for indel callers.

Finally, the authors demonstrate Scalpel's use on a large set of genetic data from nearly 600 families who donated samples to the Simons Simplex Collection, a project of the Simons Foundation Autism Research Initiative. Scalpel found a very high enrichment for indels in children affected by autism, compared with their unaffected siblings, a pattern that persisted even after excluding common variants.

Quick tour of Genetic Algorithms !

Jit — Thu, 17 Jan 2019 03:42:48 -0600

The R package GA provides a collection of general purpose functions for optimization using genetic algorithms. The package includes a flexible set of tools for implementing genetic algorithms search in both the continuous and discrete case, whether constrained or not. Users can easily define their own objective function depending on the problem at hand.

https://cran.r-project.org/web/packages/GA/vignettes/GA.html

Address of the bookmark: https://cran.r-project.org/web/packages/GA/vignettes/GA.html

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity

Rahul Nayak — Tue, 29 May 2018 08:37:53 -0500

The k-mer Weighted Inner Product.

This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any reference genome, and without assembling one.

De novo estimates of genetic relatedness from next-gen sequencing data https://kwip.readthedocs.org

Address of the bookmark: https://github.com/kdmurray91/kwip

DAVI: Deep learning-based tool for alignment and single nucleotide variant identification

Jit — Tue, 16 Mar 2021 05:41:33 -0500

DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools used for bench-marking. We further demonstrate that while existing tools are based on data generated from a specific sequencing technology, the models proposed in DAVI are generic and can be used across different NGS technologies as well as across different species

https://iopscience.iop.org/article/10.1088/2632-2153/ab7e19/pdf

Address of the bookmark: https://github.com/gguptaiitd/NEAT

DMINDA2: an integrated web server for DNA motif identification and analyses

BioStar — Sun, 02 Feb 2020 14:26:01 -0600

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses

More at http://bmbl.sdstate.edu/DMINDA2/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086085/

Address of the bookmark: http://bmbl.sdstate.edu/DMINDA2/

fastv - detect virus

Jit — Sat, 11 Dec 2021 08:04:10 -0600

fastv is an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. It detects microbial sequences from FASTQ data, generates JSON reports and visualizes the result in HTML reports. This tool can be used to detect viral infectious diseases, like COVID-19. This tool supports both short reads (Illumina, BGI, etc.) and long reads (ONT, PacBio, etc.)

Address of the bookmark: https://github.com/OpenGene/fastv

SISRS: Site Identification from Short Read Sequences

Abhimanyu Singh — Wed, 28 Nov 2018 08:56:03 -0600

Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads must have a fastq file extension.

Address of the bookmark: https://github.com/rachelss/SISRS

ENCODE3: A collection of research articles and related content describing the Encyclopedia of DNA Elements, its datasets and tools.

Shruti Paniwala — Sat, 08 Aug 2020 08:25:21 -0500

How cells, tissues and organisms interpret the information encoded in the genome has vital implications for our understanding of development, health and disease. Launched in 2003, the ENCyclopedia Of DNA Elements (ENCODE) project has the aim of mapping the functional elements in the human genome (later expanded to include model organisms).

During the first phase of ENCODE, published in 2007, microarray-based technologies were used to detect regions associated with transcription factors, certain histone modifications and open chromatin within a pre-specified 1% of the human genome.

ENCODE’s second phase saw a switch to sequencing-based technologies, the addition of new assay types and the analysis of functional elements genome-wide, described in a collection of research articles in 2012.

The Encyclopedia paper of ENCODE 3, published in Nature, gives an overview of the various assays that were performed in human and mouse cell lines and tissues and describes a Registry of human and mouse candidate cis-regulatory elements (cCREs).

More at https://www.nature.com/immersive/d42859-020-00027-2/index.html

Josefa González Lab

Thu, 19 Aug 2021 08:52:56 -0500

Lab focus on understanding how organisms adapt to their environments. They combine omics approaches with detailed molecular and phenotypic analyses to get a comprehensive picture of adaptation. Our aim at being internationally recognized as a leading lab in the field of environmental adaptation.
Lab share our passion for science with the general public by leading outreach projects aimed at increasing science awareness.

More at https://www.biologiaevolutiva.org/gonzalez_lab/