Error Reads
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Access Genome assembly using Nanopore-guided long and error-free DNA readsMohammed-AminMadoui†1, StefanEngelen†1, CorinneCruaud1, CarolineBelser1, LaurieBertrand1, AdrianaAlberti1, ArnaudLemainque1, PatrickWincker1, 2, 3 odometer reads error and Jean-MarcAury1Email author†Contributed equallyBMC Genomics201516:327DOI: 10.1186/s12864-015-1519-z© Madoui et al.; licensee obd2 reads error BioMed Central.2015Received: 15January2015Accepted: 10April2015Published: 20April2015 Abstract Background Long-read sequencing technologies were launched a few years
Illumina Error Rate
ago, and in contrast with short-read sequencing technologies, they offered a promise of solving assembly problems for large and complex genomes. Moreover by providing long-range information,
Sequencing Error Rate
it could also solve haplotype phasing. However, existing long-read technologies still have several limitations that complicate their use for most research laboratories, as well as in large and/or complex genome projects. In 2014, Oxford Nanopore released the MinION® device, a small and low-cost single-molecule nanopore sequencer, which offers the possibility of sequencing next-gen sequencing error rate long DNA fragments. Results The assembly of long reads generated using the Oxford Nanopore MinION® instrument is challenging as existing assemblers were not implemented to deal with long reads exhibiting close to 30% of errors. Here, we presented a hybrid approach developed to take advantage of data generated using MinION® device. We sequenced a well-known bacterium, Acinetobacter baylyi ADP1 and applied our method to obtain a highly contiguous (one single contig) and accurate genome assembly even in repetitive regions, in contrast to an Illumina-only assembly. Our hybrid strategy was able to generate NaS (Nanopore Synthetic-long) reads up to 60kb that aligned entirely and with no error to the reference genome and that spanned highly conserved repetitive regions. The average accuracy of NaS reads reached 99.99% without losing the initial size of the input MinION® reads. Conclusions We described NaS tool, a hybrid approach allowing the sequencing of microbial genomes using the MinION® dev
takes the raw read sequences produced by a
Celera Assembler
next generation sequencing platform like machines from Illumina pubmed or Roche. SEECER removes mismatch and indel errors from the raw reads google scholar and significantly improves downstream analysis of the data. Especially if the RNA-Seq data is used to produce a de novo http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1519-z transcriptome assembly, running SEECER can have tremendous impact on the quality of the assembly. News Version 0.1.3 of SEECER is available now. Improved error handling of SEECER pipeline. Update to Jellyfish version 1.1.11. This should fix problems with some of the http://sb.cs.cmu.edu/seecer/ bigger datasets where the pipeline crashed. Date: 10/2/2013 · Tags: version 0.1.3 The paper has been published: Probabilistic error correction for RNA sequencing, Nucleic Acids Research (2013). Date: 4/05/2013 · Tags: paper Version 0.1.2 of SEECER is available now. fixed an issue with processing some FastQ files. Date: 2/10/2013 · Tags: version 0.1.2 Version 0.1.1 of SEECER is available now. removed warnings to avoid compiler problems on Ubuntu improved scalability because parallelization is now lock-free to support machines with many cores Date: 6/27/2012 · Tags: version 0.1.1 References Hai-Son Le, Marcel H. Schulz, Brenna M. McCauley, Veronica F. Hinman and Ziv Bar-Joseph. Probabilistic error correction for RNA sequencing. Nucleic Acids Research (2013) Copyright © 2012 · Template design by Andreas Viklund
Sign in Pricing Blog Support Search GitHub This repository Watch 17 Star 115 Fork 38 marcelm/cutadapt Code Issues 19 Pull requests 3 https://github.com/marcelm/cutadapt/issues/199 Projects 0 Pulse Graphs New issue error: Reads are improperly paired. while the reads are properly paired #199 Closed ranijames opened this Issue May 12, 2016 · 4 comments https://www.youtube.com/watch?v=FBhaxnw8Rl0 Projects None yet Labels None yet Milestone No milestone Assignees No one assigned 2 participants ranijames commented May 12, 2016 Hello All, I have downloaded file error rate from SRA which I converted into fastq files using fastq-dump. Now when I try to remove the adapter sequences using cut-adapt. it's throwing me following error, cutadapt: error: Reads are improperly paired. Read name 'SRR2040271.1.1 SN603_WBP007_8_1101_63.30_99.90 length=100' in file 1 does not match 'SRR2040271.1.2 SN603_WBP007_8_1101_63.30_99.90 length=100' in file 2. For me, both fastq files have properly paired reads. sequencing error rate file_1.fastq, @SRR2040271.1.1 SN603_WBP007_8_1101_63.30_99.90 length=100 NTCATTCCATGACATTGTCTGTTGGTTGCTTTTTGAGTATATTTTCTCATGGCTTCATCTATCTTGCTCATAAGACTAAATGGGGAGACAGACTTCCTGG +SRR2040271.1.1 SN603_WBP007_8_1101_63.30_99.90 length=100 !1=DDFFFGHHHHIJJJJJIIJJJGGHJGJIJJGBGGHEGHJIIIIEHIJEH>@G;FHCG
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