BOL: Related items

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

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

Flye: Fast and accurate de novo assembler for single molecule sequencing reads

Rahul Nayak — Sat, 06 Jul 2019 03:48:22 -0500

Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.

Address of the bookmark: https://github.com/fenderglass/Flye

Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?

Rahul Agarwal — Wed, 17 Jul 2013 15:25:09 -0500

Like in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete de novo assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?

Genome Browsers

Rahul Agarwal — Fri, 16 Aug 2013 19:04:47 -0500

Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc.

Following are the weblink for different available browsers:

http://www.ensembl.org/index.html

http://ensemblgenomes.org/

http://genome.ucsc.edu/

http://www.ncbi.nlm.nih.gov/genome

http://www.ebi.ac.uk/genomes/

http://flybase.org/

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

http://www.sanger.ac.uk/resources/databases/

How Genes are Regulated: Transcription Factors

Thu, 05 Sep 2013 16:54:19 -0500

Each cell in our body inherits the same master copy of DNA, but different cell types use it differently. Transcription Factors help influence which genes are used in which cell. Understanding how these dynamic proteins physically interact with DNA allows us to better understand and model their binding to DNA and their regulation of gene expression. Scientific Direction by the Wasserman Lab at the University of British Columbia: http://www.cmmt.ubc.ca/research/investigators/wasserman/lab Animation and editing by Blair Lyons of Stroma Studios: http://www.stromastudios.com

Molecular Genetics Lecture

Rahul Agarwal — Fri, 27 Sep 2013 04:24:45 -0500

"Robert Sapolsky makes interdisciplinary connections between behavioral biology and molecular genetic influences. He relates protein synthesis and point mutations to microevolutionary change, and discusses conflicting theories of gradualism and punctuated equilibrium and the influence of epigenetics on development theories."

"Robert Sapolsky is an American neuroendocrinologist, professor of biology, neuroscience, and neurosurgery at Stanford University, researcher and author" ----Wikipedia

Address of the bookmark: http://www.youtube.com/watch?v=_dRXA1_e30o

Edit DNA !!!

Jit — Wed, 05 Mar 2014 02:27:54 -0600

A genome-engineering tool known as Crispr may allow scientists to alter the DNA of humans, animals and plants, a research breakthrough that promises to make a significant impact on science and fighting diseases, according to a March 3 story in the New York Times. Scientists hope Crispr might also be used for genomic surgery, as it were, to correct errant genes that cause disease.

A rescently publication paper ( http://jb.asm.org/content/169/12/5429.long )shows significance of an unusual repeated DNA sequences next to a gene in a common bacterium, and their scientific significance. The sequences, it turns out, are part of a sophisticated immune system that bacteria use to fight viruses. And that system, whose very existence was unknown until about seven years ago, may provide scientists with unprecedented power to rewrite the code of life. This means a genome can be edited, much as a writer might change words or fix spelling errors. It allows “customizing the genome of any cell or any species at will,”.

Reference:

http://www.prweb.com/releases/2014/03/prweb11636031.htm

http://www.nytimes.com/2014/03/04/health/a-powerful-new-way-to-edit-dna.html?hpw&rref=health

http://jb.asm.org/content/169/12/5429.long

methylKit

Jit — Fri, 03 Jun 2016 10:09:29 -0500

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal with base-pair resolution data for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome bisulfite sequencing data if proper input format is provided.

Address of the bookmark: https://github.com/al2na/methylKit

Software and Tools to detect structure variation with long reads !!

Archana Malhotra — Wed, 15 Mar 2017 14:31:09 -0500

Uncovering the connection between genetics and heritable diseases requires an approach that looks at all the variant bases and types in a genome. While a PacBio de novo assembly resolves the most novel SV variants. 8-10X PacBio coverage of single genomes or trios reveals triple the SVs detectable by short-read data.

With Single Molecule, Real-Time (SMRT) Sequencing, you can access structural variations having a broad range of sizes, types, and GC content with the ability to:

Uncover missing heritability linked to structural variation
Unambiguously identify genomic context and variant breakpoints at the sequence level to unravel the genetic etiology of disease
Resolve structural variation across the complete size spectrum with basepair resolution

Following are the SV tools, which can assist you to achieve your goal.

Sniffles: Structural variation caller using third generation sequencing

Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires sorted output from BWA-MEM (use -M and -x parameter) or NGM-LR with the optional SAM attributes enabled!

More at https://github.com/fritzsedlazeck/Sniffles

MultiBreak-SV: It identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.

There are two pieces of software in this release: (1) a pre-processor that takes machineformat (.m5) BLASR files, and (2) MultiBreak-SV. For installation and usage instructions, see doc/MultiBreakSV-Manual.txt.

More at https://github.com/raphael-group/multibreak-sv

Parliament: A Structural Variation Tool. Why ask a single sv-detection approach to find every variant when you can have a parliament of tools deciding?

Publication about the algorithm and “…the first long-read characterization of structural variation in a diploid human personal genome…” (HS1011) - “Assessing structural variation in a personal genome—towards a human reference diploid genome”

More at https://sourceforge.net/projects/parliamentsv/

https://www.dnanexus.com/papers/Parliament_Info_Sheet.pdf

PBHoney: the structural variation discovery tool

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

Read The Paper http://www.biomedcentral.com/1471-2105/15/180/abstract

More at https://sourceforge.net/projects/pb-jelly/

SMRT-SV: Structural variant and indel caller for PacBio reads

Structural variant (SV) and indel caller for PacBio reads based on methods from Chaisson et al. 2014.

SMRT-SV provides an official software package for tools described in Chaisson et al. 2014 and adds several key features including the following.

Unified variant calling user interface with built-in cluster compute support
Small indel calling (2-49 bp)
Improved inversion calling (screenInversions)
Quality metric for SV calls based on number of local assemblies supporting each call
Higher sensitivity for SV calls using tiled local assemblies across the entire genome instead of "signature" regions
Genotyping of SVs with Illumina paired-end reads from WGS samples

More at https://github.com/EichlerLab/pacbio_variant_caller