BOL: Related items

Introduction of Epigenomics

Rahul Agarwal — Sun, 06 Oct 2013 04:59:30 -0500

Address of the bookmark: http://www.genome.gov/27532724

A-allele of SLC24A5 gene is found to be responsible for variation in skin color of South-East Asians and Europeans

Rahul Agarwal — Tue, 12 Nov 2013 21:02:27 -0600

Key finding:

rs1426654 SNP of SLC24A5 gene is decider of skin pigmentation variation in South Asia
rs1426654-A allele is widely spread throughout the Indian subcontinent
Skin pigmentation is also account by the combination of processes like selection and demographic history of populations affected by their language and origin
Sign of positive selection in Europeans, Middle East, Pakistan, Central Asia and North India but not in South India
In European , A-allele is almost reached to fixation

Paper:

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003912

Your stress/depression came from ancestor

Rahul Agarwal — Sun, 04 May 2014 18:46:20 -0500

"A study published in Nature Neuroscience finds that stress in early life alters the production of small RNAs, called microRNAs, in the sperm of mice. The mice show depressive behaviours that persist in their progeny."

Source:

http://www.nature.com/news/sperm-rna-carries-marks-of-trauma-1.15049

GeneProf: analysis of high-throughput sequencing experiment

Jit — Wed, 05 Jul 2017 16:47:05 -0500

GeneProf is a web-based, graphical software suite that allows users to analyse data produced using high-throughput sequencing platforms (RNA-seq and ChIP-seq; "Next-Generation Sequencing" or NGS): Next-gen analysis for next-gen data!

Some of GeneProf's highlights include:

Easy-to-use web-based interface:Access your data at any time from any computer with a working internet connection -- no need to install software! (cp. Section 'System Requirements').
Analysis wizards make your life easy:Step-by-step workflows make it easy to analyse high-throughput data within a minimum of hands-on time. (cp. SubConcept 'Analysis Wizards').
Versatile modules:Advanced users and data analysis experts benefit from GeneProf's broad range of analysis modules, which can be combined freely into sophisticated workflows (cp. Concept 'Workflows').
Integrated Analysis:Analysis of ChIP-seq and RNA-seq data in one place, plus support for the integration of other external data (e.g. from microarrays).
Comprehensive Resource:GeneProf provides a comprehensive resource of fully analyzed next-generation sequencing data. Experimental results can be easily accessed and compared and the analysis procedures employed to produce the data are fully transparent (cp. Tutorial 'Examining Public Next-Gen Data..').
Extensibility:Algorithm developers and computer programmers can develop their own modules and extend GeneProf. Existing software can be easily wrapped in the workflow framework (cp. Section 'Module Development: Adding new..') and data from GeneProf may be used externally (cp. Section 'Web API: Retrieving Data from ..').

GeneProf is academic software developed at the Centre for Regenerative Medicine / Institute for Stem Cell Research, University of Edinburgh and has benefited from funding by the Medical Research Council and the EU Framework 7 Project "EuroSyStem".

Address of the bookmark: https://www.geneprof.org/GeneProf/index.jsp

AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing

BioStar — Fri, 22 Dec 2017 00:31:06 -0600

AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to conventional public pipelines and ∼48% to the in-house commercial solution, with a minimal loss of sensitivity

The program with a detailed manual is available at https://sourceforge.net/projects/airvf/

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

d2Tools: The toolbox for counting the frequency of k-tuple from sequencing datasets and calculate the dissimilarity

Jit — Thu, 20 Sep 2018 08:38:29 -0500

d2Tools are the toolbox for counting the frequency of K-tuple from sequencing datasets and then calculating the pairwise dissimilarity matrix between samples with the d2-style(d2/d2*/d2S representing d2/d2Star/d2shepp, respectively) measures. Hao, Dai, Eucliean, Mahattan, and Chebyshev distance measures are also included in d2Tools.

Manual at https://code.google.com/archive/p/d2-tools/wikis/d2ToolMannual.wiki

Address of the bookmark: https://code.google.com/archive/p/d2-tools/

Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data

Jit — Tue, 22 Jan 2019 06:26:55 -0600

Run a pipeline processing fast5s to a consensus in a single command.
Recommended fixed "standard" and "fast" pipelines.
Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath.
Seemless distribution of tasks over local or distributed compute.
Highly configurable.
Open source (Mozilla Public License 2.0).

Documentation can be found at https://nanoporetech.github.io/katuali/.

Address of the bookmark: https://github.com/nanoporetech/katuali

iSeqQC: a tool for expression-based quality control in RNA sequencing

BioStar — Sun, 16 Feb 2020 08:47:17 -0600

iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering, agglomerative hierarchical clustering and correlation coefficients to provide insight into outliers.

http://cancerwebpa.jefferson.edu/iSeqQC/

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3399-8

Address of the bookmark: https://github.com/gkumar09/iSeqQC

Pollux: platform independent error correction of single and mixed genomes

Jit — Fri, 19 May 2017 09:41:27 -0500

Pollux: General-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and correct insertion, deletion, and homopolymer errors while remaining sensitive to low coverage areas of sequencing projects. Using published data sets, we correct 94% of Illumina MiSeq errors, 88% of Ion Torrent PGM errors, 85% of Roche 454 GS Junior errors. Introduced errors are 20 to 70 times more rare than successfully corrected errors. Furthermore, we show that the quality of assemblies improves when reads are corrected by our software.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0435-6

Address of the bookmark: https://github.com/emarinier/pollux

DISCO : multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler

Jit — Mon, 10 Jul 2017 10:09:27 -0500

DISCO is a multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler. Disco was developed as a scalable assembler to assemble large metagenomes from billions of Illumina sequencing reads of complex microbial communities. Disco was parallelized for computer clusters in a hybrid architecture that integrated shared-memory multi-threading, point-to-point message passing, and remote direct memory access. The assembly and scaffolding were performed using an iterative overlap graph approach.

Address of the bookmark: http://disco.omicsbio.org/