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An assembly of reads, contigs and scaffoldsA blog on all things newbler and beyond
http://contig.wordpress.com/
A blog on all things newbler and beyond
http://contig.wordpress.com/
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An assembly of reads, contigs and scaffolds | contig.wordpress.com Reviews
https://contig.wordpress.com
A blog on all things newbler and beyond
contig.wordpress.com
2010 September « An assembly of reads, contigs and scaffolds
https://contig.wordpress.com/2010/09
An assembly of reads, contigs and scaffolds. A blog on all things newbler and beyond. Enter your email address to subscribe to this blog and receive notifications of new posts by email. Join 116 other followers. Archive for September, 2010. Running newbler: de novo transcriptome assembly II: the output files. On September 21, 2010. Alternative rope splicing (source: Wikimedia commons). The differences for this file, relative to the same file for a ‘normal’ assembly (described in this post.
2011 September « An assembly of reads, contigs and scaffolds
https://contig.wordpress.com/2011/09
An assembly of reads, contigs and scaffolds. A blog on all things newbler and beyond. Enter your email address to subscribe to this blog and receive notifications of new posts by email. Join 116 other followers. Archive for September, 2011. Newbler input III: a quick fix for the new Illumina fastq header. On September 1, 2011. Source: thepoolandspashoponline.com.au). Basically, some elements have been added, some have changed order, and there are now two parts seperated by a space. Posted in Newbler input.
2010 October « An assembly of reads, contigs and scaffolds
https://contig.wordpress.com/2010/10
An assembly of reads, contigs and scaffolds. A blog on all things newbler and beyond. Enter your email address to subscribe to this blog and receive notifications of new posts by email. Join 116 other followers. Archive for October, 2010. Newbler input I: the sff file. On October 28, 2010. Newbler can obviously take in the 454 reads, but also other read types: regular Sanger reads, any sequence in a fasta file (at most 200 bp), and perhaps also Illumina reads. Or use the biopython parser. Nothing for bio...
2011 April « An assembly of reads, contigs and scaffolds
https://contig.wordpress.com/2011/04
An assembly of reads, contigs and scaffolds. A blog on all things newbler and beyond. Enter your email address to subscribe to this blog and receive notifications of new posts by email. Join 116 other followers. Archive for April, 2011. Newbler output IV: on ultra-short and single-read contigs. On April 5, 2011. Sometimes you might observe very short contigs, some even having high read depth. You might see these for example when. 8211; very deep alignments (with lots of reads) can cause shattering, cause...
2010 May « An assembly of reads, contigs and scaffolds
https://contig.wordpress.com/2010/05
An assembly of reads, contigs and scaffolds. A blog on all things newbler and beyond. Enter your email address to subscribe to this blog and receive notifications of new posts by email. Join 116 other followers. Archive for May, 2010. Newbler output VI: the ‘status’ files (454TrimStatus.txt, 454ReadStatus.txt, 454PairStatus.txt) and the 454AlignmentInfo.tsv file. On May 20, 2010. The fact that these files are tabular makes for easy parsing using by perl/python or, my favorite, awk. Build a website with W...
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Annotate: A Plugin for the Ion Torrent Browser | BioLektures
https://biolektures.wordpress.com/2011/12/29/annotate-a-plugin-for-the-ion-torrent-browser
This blog contains mainly bioinformatics analysis and discussion. Signal Processing – Room for improvements? Are MiSeq miscalls influenced by preceding homopolymers? Annotate: A Plugin for the Ion Torrent Browser. December 29, 2011. Novel versus Common Variants. Stored on the Torrent Server is ordered different to the dbSNP VCF file. From the GATK 1.2 resouce bundle. For this plugin, I have decided to index the VCF file using tabix. And call the variants outside the GATK framework. Functional Impact of N...
Ion Torrent – Rapid Software Improvements | BioLektures
https://biolektures.wordpress.com/2011/09/19/ion-torrent-rapid-software-improvements
This blog contains mainly bioinformatics analysis and discussion. The Ion Torrent Accuracy Challenge – A non-biological explanation. Ion Torrent and the Democratization of Sequencing →. Ion Torrent – Rapid Software Improvements. September 19, 2011. There are three major areas that software can improve. Throughput – Identify more Ion Sphere Particles (ISPs) with library fragments therefore increasing the total number of reads. Quality – More and longer reads aligning back to the reference sequence. The ta...
Life Grand Challenges – Innocentive but not enough Incentives (Part 3) | BioLektures
https://biolektures.wordpress.com/2011/08/18/life-grand-challenges-–-innocentive-but-not-enough-incentives-part-3
This blog contains mainly bioinformatics analysis and discussion. Life Grand Challenges Mission Impossible to Improbable (Part 2). Challenges in Improving Ion Torrent Raw Accuracy (Part 3) →. Life Grand Challenges Innocentive but not enough Incentives (Part 3). August 18, 2011. Ever used IMDB or Rotten Tomatoes as an indicator of how good a movie is and whether you should watch it? While Tekken best movie ever only got 5.0 on IMDB. Competition was open in 2006 and would end in 2011. A progress prize of 5...
Disclaimer | BioLektures
https://biolektures.wordpress.com/disclaimer
This blog contains mainly bioinformatics analysis and discussion. My thoughts, opinions and random outburst are independent and do not reflect the views of the University of Sydney or the Institute for Neuroscience and Muscle Research. In fact, most people in my lab thinks I’m nuts and my jokes are terrible. I have received free dinner! Unfortunately, the Illumina free dinner at ASHG 2011 was invite only😦. Here are the parties I have received food from and my ratings out of 10. Other Mum’s (10/10)...
Are MiSeq miscalls influenced by preceding homopolymers? | BioLektures
https://biolektures.wordpress.com/2012/02/01/are-miseq-miscalls-influenced-by-preceding-homopolymers
This blog contains mainly bioinformatics analysis and discussion. Annotate: A Plugin for the Ion Torrent Browser. Crowd Sourcing 2.0 – Smaller and Faster = Better →. Are MiSeq miscalls influenced by preceding homopolymers? February 1, 2012. A recent post in the Ion Community Torrent Dev section presents an analysis showing MiSeq systematic substitution errors which appear to be caused by preceding homopolymers (HPs). The Omics Omics blog post. 2) E coli MG1655. From a recent Genome Biology publication.
Fundamentals of base calling (Part 1) | BioLektures
https://biolektures.wordpress.com/2011/08/10/fundamentals-of-base-calling-part-1
This blog contains mainly bioinformatics analysis and discussion. Fundamentals of base calling (Prequel). Fundamentals of base calling (Part 2) →. Fundamentals of base calling (Part 1). August 10, 2011. The Ionogram of a well containing. These are raw values extracted from the 1.wells file. Note: The flow order does not follow a repeating 4 flow cycle of T. Packages to produce the plots. The Ionogram of the same well containing. Below are the bases called for this well. This was the 5th best. As this bet...
The Genome Factory: Bacterial genome annotation systems
http://thegenomefactory.blogspot.com/2013/03/bacterial-genome-annotation-systems.html
Bioinformatics tips, tricks, tools and commentary with a microbial genomics bent. Written by Torsten Seemann from Melbourne, Australia. Saturday, 30 March 2013. Bacterial genome annotation systems. You get a bacterial isolate. You sequence it. You manage to get some contigs after mucking around with some de novo. Assembly software. Now what? What is genome annotation? A gene abbreviation and an enzyme classification number. In the old days, a basic ORF. Finder would be run over the contigs. Then the ...
Developments in high throughput sequencing – June 2015 edition | In between lines of code
https://flxlexblog.wordpress.com/2015/06/17/developments-in-high-throughput-sequencing-june-2015-edition
In between lines of code. Biology, sequencing, bioinformatics and more. Developments in high throughput sequencing June 2015 edition. June 17, 2015. This is the fourth edition of this visualisation, previous editions were in June 2014. As before, full run throughput in gigabases (billion bases) is plotted against single-end read length for the different sequencing platforms, both on a log scale. Yes, I know a certain new instrument seems to be missing, hang on, I’m coming back to that…. Note how close to...
sEqUeNcE aSsEmBLy: A very important blog
http://ngsassembly.blogspot.com/2010/06/very-important-blog.html
Monday, June 21, 2010. A very important blog. Http:/ contig.wordpress.com/2010/04/13/newbler-output-iii-the-454contiggraph-txt-file/. Posted by neel oporazeeta. September 21, 2010 at 12:42 PM. Subscribe to: Post Comments (Atom). Odd number of sequences in paired end file. A very important blog. Picture Window template. Powered by Blogger.
Crowd Sourcing 2.0 – Smaller and Faster = Better | BioLektures
https://biolektures.wordpress.com/2012/04/21/crowd-sourcing-2-0-smaller-and-faster-better
This blog contains mainly bioinformatics analysis and discussion. Are MiSeq miscalls influenced by preceding homopolymers? Time stamping Steve Avery’s Blood DNA →. Crowd Sourcing 2.0 – Smaller and Faster = Better. April 21, 2012. Yes, scientific writing is the art of suggesting everything but committing to nothing😆. Thanks to everyone who visited and supported Biolektures during the non-active periods. In August, I blogged a three part series that criticized the challenge in terms of fairness. The above...
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株式会社 コンティグ・アイ
日時 2014年3月30日 日 4月12日 土. 協賛 竹市電機株式会社 株式会社コンティグ アイ. 雑草 芝生 シュレッダー等の廃棄物 植物性セルロース から精製したバイオエタノールを利用して発電機で発電し、LEDイルミネーションを点灯します。 イルミネーション点灯期間は3月30日 日 12日 土 日没頃 21 00の間で行います。 ２０１３年１１月３０日 土 に、美濃加茂市の蜂屋小学校で わくわくサイエンスDAY が開催され、当社は理科室を使ってバイオエタノール生産体験を行いました。 環境浄化植物 サンパチェンスからバイオエタノールを製造しました 協力 株式会社サカタのタネ. 受付 13 30 開始 14 00 16 00. 今後、本格的な除染作業等が始まり次第、減容 除染 放射物質回収だけでなく、同時に副生成物としてのバイオエタノールと肥料の生産を安価に行える新規性のある弊社技術を用いて、国 環境省 福島県の施策である再生可能エネルギーの開発 利用促進に貢献できると考えております。 弊社が開発したLocked Nucleic Acid-1 固定化核酸-1 を使った化粧品が販売されました。
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An assembly of reads, contigs and scaffolds
An assembly of reads, contigs and scaffolds. A blog on all things newbler and beyond. Enter your email address to subscribe to this blog and receive notifications of new posts by email. Join 115 other followers. Cross-posted: make Newbler open source. On January 31, 2014. Cross posted from flxlexblog.wordpress.com. Having used the Newbler program with a hybrid 454 and Illumina dataset to improve upon the human genome. To get a free copy of the software. Still, this has hampered the wide-spread adopti...
Blog de Contig0 - Rien N'est Plus Vivant Qu'un Souvenir______________*REMEMBER! - Skyrock.com
Mot de passe :. J'ai oublié mon mot de passe. Rien N'est Plus Vivant Qu'un Souvenir *REMEMBER! Si on fait le vide autour d'un souvenir, il ne reste plus rien que ce souvenir dans l'infini qu'on a, et ce souvenir devient l'infini. Ce livre est écrit beaucoup avec le rêve, un peu avec le souvenir. Rêver est permis aux vaincus ; se souvenir est permis aux solitaires. On ne recommence plus, mais se souvenir, c'est presque recommencer. Je vous aimes (L'. Mise à jour :. Abonne-toi à mon blog! E de Louis 3.
Mr. Contiga: BLOG (v.2)
Mr Contiga: BLOG (v.2). Monday, October 17, 2011. Farewell BLOG.thank you for everything. Making mistakes are okay, as long as you learn from them.". This blog will no longer be used starting today. I am now using a new blog, here is the link:. Http:/ contiga.edublogs.org/. The new blog allows you to download any files that I attach to a message (for example, if you are away and need a copy of the debate template, you can easily click on the link and either open/save that file into your own computer.
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