Next Generation Sequencing's Blog

Laboratory Technician – Next Generation Sequencing

nextgenerationsequencing — Wed, 07 Jul 2010 22:43:37 +0000

We are hiring again. The California office needs to fill a position for laboratory technician/research associate. The position requires experience with Illumina next generation sequencing technology. Visit the EG site for more details.

Next Generation Sequencing

nextgenerationsequencing — Fri, 15 Jan 2010 17:08:31 +0000

Eureka Genomics wishes everyone a Happy New Year!

Visit them for your next generation sequencing or bioinformatics needs.

Eureka Genomics Now Provides Gene Annotation

nextgenerationsequencing — Mon, 28 Dec 2009 22:34:57 +0000

Eureka Genomics now provides gene annotation along with high-throughput sequencing and bioinformatics.

Linux Commands for Bioinformatics

nextgenerationsequencing — Wed, 18 Nov 2009 17:06:04 +0000

I am always having to replace certain text strings in html files that our bioinformatics software produces. Here is an easy command that does the job. I have to admit I probably picked this one up somewhere on the net. I would test it without the -i switch first and as long as everything looks good do the inline editing with -i. Make sure you always have backups!

Search and Replace string in all files in directory
grep -rl matchstring somedir/ | xargs sed -i ’s/string1/string2/g’

If you are interested in advanced bioinformatics and next generation sequencing services, please visit my employer. I am sure they would be happy.

Velvet Sequence Assembler

nextgenerationsequencing — Tue, 17 Nov 2009 19:01:45 +0000

Velvet is an open source sequence assembler that does a good job with short reads. There site states this fact in the opening page. This is probably the best free alternative to working with next generation sequencing data. The organization that employs me uses proprietary technology that is licensed from the University of Houston to produce our data sets but we have used Velvet on occasion, mainly for testing purposes.

Download multiple FASTA files from NCBI

nextgenerationsequencing — Tue, 17 Nov 2009 18:02:00 +0000

Here is how I download nucleotide fasta files from NCBI. You can implement this into a Perl script to automate multiple retrievals.

wget -O example.fa http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&qty=1&c_start=1&list_uids=49175990&itemID=3593&dopt=fasta&send=Send&sendto=t&extrafeatpresent=1&ef_MGC=16

If you are interested in bioinformatics and next generation sequencing you can visit the company I work for at the link provided.

Next Generation Sequencing

nextgenerationsequencing — Fri, 13 Nov 2009 22:50:32 +0000

I will be posting my shortcuts for bioinformatics and next generation sequencing work. I hope someone can benefit from the posts.