Results for "QC"
Blogs
BBTools for bioinformatician !
...s: Code: $ reformat.sh in=reads.fastq out1=r1.fastq out2=r2.fastq Base quality histograms Code: $ reformat.sh in=reads.fq qchist=qchist.txt That stands for "q...2267 days ago
Basic command-line to run BLAST
...ord_size int_value] [-gapopen open_penalty] [-gapextend extend_penalty] [-qcov_hsp_perc float_value] [-max...open_penalty] [-gapextend extend_penalty] [-perc_identity float_value] [-qcov_hsp_perc float_value] [-max...2241 days ago
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Bookmarks
- ...ontent per sequence GC content per sequence quality sequence length distribution More at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
2939 days ago
HOMER: Software for motif discovery and next-gen sequencing analysis
This tutorial covers topics independently of HOMER, and represents knowledge which is important to know before diving head first into more advanced analysis tools suc...2928 days ago
- +17 more Bookmarks
Pages
Virtual Bioinformatics Online Tutorial
There are several vitual online bioinformatics training centres. Here I provide some of them: Virtual Institute of BioinformaticsNational University of Ireland , I...3918 days ago
Genome Assembly Tools and Software - PART2 !!
...riant calls from the latest 250 base Illumina PCR-free fragment reads. SeqCons 1.0 – de novo and reference-guided Sequence Assembly SeqCons (Sequence consensus)...2682 days ago
Top-level pages
Best book Titles for Learning Bionformatics
...60545 http://www.amazon.com/Introduction-Bioinformatics-Algorithms-Computational-Molecular/dp/0262101068 http://books.google.no/books?id=pxSM7R1sdeQC&dq=Pierre+baldi+%2B+bioin...3914 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...cing data. Cox et al, BMC Bioinformatics 11:485, 2010. PubMedCentral TileQC: a system for tile-based qual...uencing errors. Kelley et al, Genome Biol 11(11):R116, 2010. PubMed FastQC: a quality control tool for h...3776 days ago
- +7 more Top-level pages
Wire posts
News
You and your friend have similar DNA !!!
New research out of Massachusetts claims that people often choose friends that are similar to them in genetics and they are more accurate than you might suppose. A st...3566 days ago
- ...this webinar, we will highlight the UMI-friendly features of Strand NGS v3.1 including support for handling well known and customised UMI libraries, QC metrics, consensus alignment,...
2368 days ago
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Opportunity posts
- ...: Programming: Perl and Python. Operating system: Linux and Windows. NGS Analysis tools: Maq, BWA, Bowtie, SAM tools, BEDTools, MACS, Galaxy, FastQC, Bismark, MEDIPS, Tophat, Cuf...
3162 days ago
Scientist - Computational Genomics (Two Positions)
...calability, robustness and user experience. Implement and oversee the QA/QC practices to ensure the devel...High Performance Computing, data architecture, database platforms and QA/QC practices in software enginee...2972 days ago
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ResearchLabs posts
Page Lab at Whitehead Institute, MIT
...igins of gametes, and infertility. PI webpage : http://pagelab.wi.mit.edu/david_page.html Ted Presentation : http://www.youtube.com/watch?v=nQcgD5DpVlQ Lab webpage: http:...3916 days ago
Bio-Scripts
BASH script for SelfBLAST a genome
...ery $SEQ -db $MYDB -evalue 1e-5 -num_threads $THREAD -max_target_seqs 1 -outfmt '6 qseqid staxid qstart qend sseqid sstart send evalue length frames qcovs' -out $OUTFILE; echo "D...2649 days ago
- library(vcfR) # Input the files. vcf
2057 days ago
- +8 more Bio-Scripts
Tags
- Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step Blaxter Lab, Institute of Evolutionary Biology, University of Edinburgh Goal: To create blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to...
Tags: Bioinformatics, Blobology, Blobplot, TAGC Plot, GC, Assembly, NGS, QC
2880 days ago
MinION_GC: An R script to do some QC on MinION data
Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out there: it takes about a minute to analyse a 4GB flo...Tags: MinION_GC, R, script, QC, MinION, data
2342 days ago
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Comments
Comment on "Short-read assembly using Spades !"
...of high quality and do not contain sequencing errors or low-quality bases. This step can be performed using various tools such as Trimmomatic or FastQC. Running SPAdes: After q...412 days ago
Comment on "Running Trinity on RNA-seq !"
Once your assembly is complete, there are several analyses you will likely want to pursue to explore aspects of the biology of your organism based on your assembled t...2120 days ago
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