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...2270 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...2243 days ago
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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...2930 days ago
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...3920 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)...2685 days ago
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...3917 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...3778 days ago
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...3569 days ago
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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...2975 days ago
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:...3919 days ago
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...2651 days ago
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Tags: Bioinformatics, Blobology, Blobplot, TAGC Plot, GC, Assembly, NGS, QC
2882 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
2344 days ago
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...414 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...2122 days ago