Results for "split reads"
Blogs
Computer simulation of genetic mechanism !!
Computer simulation is the discipline of designing a mode...m A tool to generate collections of synthetic reads that reflect the diverse taxo.../ pIRS Profile-based Illumina pair-end reads simulator https://code.google...2960 days ago
Various scholarships around the world !!
This page provides information on scholarships for developing countries ...plication Deadline: November 9th Commonwealth Split-site (PhD) Scholarships for D...urses: Scholarships are available for pursuing Split...2802 days ago
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Bookmarks
Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation
We demonstrate a novel approach forlocal alignment of DNA reads with respect to reference genome.For this process we have used Skip-gram model for creatingencoding(Nucl2Vec) and k-nearest neighbor...1131 days ago
Comparison of Short Read De Novo Alignment Algorithms
Excellent article to introduce different sequencing methods along with tools for de novo assembly of sequencing reads and their relevant references. Title: Comparison of Short Read De Novo Alignment Algorithms Author: Nikhil Gopal3895 days ago
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Files
Bioinformatics approach to Boar Taint
Meat products obtained from intact male pigs often produce offensive smell or odour w...taint levels were done in Illumina HiSeq2000 to >10X average coverage. Short reads generated from these samples...3774 days ago
- ...ng "OPERA-LG_v2.0.5/bin/preprocess_reads.pl" and have the following er...Finding the SA coordinates of the reads using BWA aln...[Thu Jun 14 1...FALCON-Unzip-Scaff.bamMapping long-reads using blasr.../home/urbe/Tool...c 40 -m 1 -minMatch 5 -bestn 10 -noSplitSubreads -advanceExactMatches...
2136 days ago
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Pages
Genome Assembly Tools and Software - PART2 !!
The genome assemblers generally take a file of short sequence reads and a file of quality-value a...xpression levels from RNA-Seq reads. MaLTA – Transcriptome...ose contigs can be individual reads from a subset of the paired-r...ended for Illumina sequencing reads. Quake adopts the k-mer error...2671 days ago
Awesome perl frameworks, libraries and software - PART 4
tjstein/php5-fpm-munin-plugins - A set of Munin pl...chetop is a console-based tool for monitoring the threads and overall performance of a...put-nginx-module - This is a nginx module that reads HTTP POST and PUT request bod...2479 days ago
Top-level pages
- "Bioinformatics is a science of biological predictions and analysis" -- Jitendra Narayan "The mathematical, s...enomes. Also the detection of gene fusion and gene fission (i.e, one protein is split...
3932 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
Global overview papers Next genera...Compression of DNA sequence reads in FASTQ format. Deorowicz &a...FASTX-toolkit: FASTQ/A short-reads pre-processing tools Home Pag...n FM-index of the 1.2 billion reads] Readjoiner: a fast and memo...sis of the resulting sequence reads.] Genotyping by sequencing...3764 days ago
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Wire posts
News
Illumina reveals first dataset of long reads
With the help of Moleculo technology , acquired by Illumina releases new service for long reads sequencing i.e., FastTrack Long Reads. Average read length is arou...eck following pages for publications on long reads and more: http://www.illumin...3893 days ago
RNA-Seq Data Pathway and Gene-set Analysis Workflows
It describe the GAGE (Luo et al., 2009) /Pahview (Luo and Brouwer, 2013) workflows on...e-set Analysis Workflows“. First cover a full workflow from preparation, reads counting, data preprocessing,...3818 days ago
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Opportunity posts
Research Fellow @ Mendel laboratory
IRCCS Casa Sollievo della Sofferenza – Mendel laboratory is seeking one talented bioi..., RNA-Seq and miRNA-Seq data. Main activities will be: (i) data analysis (short-reads mapping, variants call and an...3798 days ago
- INDIAN INSTITUTE OF SPICES RESEARCH (Indian Council of Agricultural Research...r conversions. 2. Assessing the quality of data and filtering of raw reads. 3. Assembling the raw reads-de novo as well as reference...
3628 days ago
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ResearchLabs posts
- The laboratory is focused on the discovery and analysis of structural variation (SVs) from genomic sequence data. A...eletions and duplications through analysis of the read depth-of-coverage; (iii) split...
2978 days ago
Video
Genetics, epigenetics and disease
Royal Society GlaxoSmithKline Prize Lecture given by Professor Adrian Bird CBE FMedSc...the autism spectrum disorder Rett syndrome is caused by loss of a protein that reads methylated CG and affects the...3858 days ago
Bio-Scripts
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.org/ has mo...Entrez.efetch(db='nucleotide',id=nm, rettype = 'fasta', retmode= 'text').read().split...1121 days ago
Perl script to count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence
#!/usr/local/bin/perl -w # While executing this script it asks for the file name of the DNA sequence. If the seq...); print " \n The original DNA file is:\n $DNA \n"; $DNA =~ s/\s//g; @DNA = split...2901 days ago
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Polls
Which of the following programming language is best for a bioinformatics beginner?
I will be doing NGS in the course of my research work and I will like to learn a...informatics tools or software. I basically want to do de-novo assembly, map reads, align reads, and expression analysis. Rec...3516 days ago
Tags
Quick next generation sequencing (NGS) terms definition
fragment size: the Illumina WGS protocol generates paired-end reads from both ends of longer fragments. The lengths of these fragments are assumed to be sampled from a normal distribution. Therefore, in the absence of structural variants, mapping locations of the paired ends span within an i...Tags: Quick, NGS, definition, fragment size, concordant reads, discordant reads, split reads, read depth
2507 days ago
Comments
Comment on "REAPR: a universal tool for genome assembly evaluation"
...ssembly based on incongruently mapped reads. It is heavily based on too low span coverage, or reads mapping too far or too close...s a list of all “perfect” reads. This is reads that have a pe...w we’ll stick to looking at the split output file, called 04.b...1322 days ago
Comment on "Installing Porechop on Ubuntu !"
...choppedNcorrected.fa Loading reads/media/urbe/MyDDrive/ONTdata/allONT/allONT.fasta1,634,477 reads loaded Looking for known ada...00.0%) 1,150,024 / 1,634,477 reads had adapters trimmed from the...1,202 / 1,634,477 reads were split based on middle adapters Out...2091 days ago
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