Results for "Reads"
Users
About me: ...er fungal pathogen challenges and genome duplication. Experienced in using next-generation sequencing technologies like shotgun sequencing, linked reads, and long-read sequencing for...1123 days ago
Blogs
Computer simulation of genetic mechanism !!
...popgen MetaSim A tool to generate collections of synthetic reads that reflect the diverse taxo...goldman-srv/phylosim/ pIRS Profile-based Illumina pair-end reads simulator https://code.google...2959 days ago
- ...t-analytical workflows in Strand NGS allow users to execute sequence analysis with stringent filtering to eliminate false positive and low quality reads. This simplifies the analysis...
2787 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-ne...1130 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 Gopal3894 days ago
- +292 more Bookmarks
Files
Bioinformatics approach to Boar Taint
...ong to Norwegian Landrace (NL) and Duroc (D) pigs with varied boar taint levels were done in Illumina HiSeq2000 to >10X average coverage. Short reads generated from these samples...3773 days ago
- ...r I'm running "OPERA-LG_v2.0.5/bin/preprocess_reads.pl" and have the following er...:18:35 2018] Finding the SA coordinates of the reads using BWA aln...[Thu Jun 14 1...arySam > FALCON-Unzip-Scaff.bamMapping long-reads using blasr.../home/urbe/Tool...
2135 days ago
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Pages
Genome Assembly Tools and Software - PART2 !!
...me information and paired-end reads. DISCOVAR 51750 – Geno...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...2669 days ago
Awesome perl frameworks, libraries and software - PART 4
...Apachetop - apachetop is a console-based tool for monitoring the threads and overall performance of a...batch calio/form-input-nginx-module - This is a nginx module that reads HTTP POST and PUT request bod...2478 days ago
Top-level pages
Useful Publications and Websites for Deep Sequencing Data Analysis
...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...3763 days ago
List of generic simulation software/tools/resource with brief description and homepage !!!
...unt.sourceforge.net/MetaSim A tool to generate collections of synthetic reads that reflect the diverse taxo...e evolution http://bit.ly/rlsim-gitpIRS Profile-based Illumina pair-end reads simulator https://code.google...3721 days ago
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Wire posts
News
Illumina reveals first dataset of long reads
...hnology , acquired by Illumina releases new service for long reads sequencing i.e., FastTrack Long Reads. Average read length is arou...You can also check following pages for publications on long reads and more: http://www.illumin...3892 days ago
RNA-Seq Data Pathway and Gene-set Analysis Workflows
...0) now includes a new tutorial, “RNA-Seq Data Pathway and Gene-set Analysis Workflows“. First cover a full workflow from preparation, reads counting, data preprocessing,...3817 days ago
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Opportunity posts
Research Fellow @ Mendel laboratory
...a range of hot applications and projects, dealing with microarrays, RNA-Seq and miRNA-Seq data. Main activities will be: (i) data analysis (short-reads mapping, variants call and an...3797 days ago
- ...of work : 1. Analysis of different file formats and their conversions. 2. Assessing the quality of data and filtering of raw reads. 3. Assembling the raw reads-de novo as well as reference...
3627 days ago
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Video
Genetics, epigenetics and disease
...Defects in signalling by CG are implicated in disease. For example, the autism spectrum disorder Rett syndrome is caused by loss of a protein that reads methylated CG and affects the...3856 days ago
Bio-Scripts
- P
2855 days ago
- # Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19
2248 days ago
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Polls
Which of the following programming language is best for a bioinformatics beginner?
...to learn a programming language which is compatible with most bioinformatics tools or software. I basically want to do de-novo assembly, map reads, align reads, and expression analysis. Rec...3514 days ago
Tags
Run miniasm assembler on nanopore reads !
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. I...Tags: Run, miniasm, assembler, nanopore, reads
2314 days ago
Frequent Paired-end reads (PE 2x100) mapping command lines
bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ && bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq > r12.bwa.sam bwa bwasw ../index/bwa/hs37m.fa r12.fq > r12.bwasw.sam ...Tags: Frequent, Paired-end, reads, (PE 2x100), mapping, command, lines
2166 days ago
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Comments
Comment on "A quick guide to Phred scaling"
...representing the quality scores of sequencing reads. It is used to quantify the p...is a common format used for storing sequencing reads. Each quality score is repres...representing the quality scores of sequencing reads, where higher scores indicate...399 days ago
Comment on "Short-read assembly using Spades !"
...quence from a large number of short sequencing reads. SPAdes (St. Petersburg genom...mbly using SPAdes: Quality control of raw reads: Before running the assembly,...ows: spades.py -o output_directory -1 forward_reads.fastq -2 reverse_reads.fastq...399 days ago
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