ABI SOLiD softwares: SOLiD Bioinformatics Workshop Part III

During the workshop, Dr. Sun presented some unpublished data on de novo genome assembly of rice blast fungus with a size ~40Mb. Partek Genomic Suite which is a third party software that can handle SOLiD data has been demonstrated. Generally, it performs gene expression analysis. It can run on all OS and requires minimum RAM.

We were then introduced to SOLiD Software Community. SOLiD suers can download a variety of data analysis tools from http://solidsoftwaretools.com for free. Tools available includes secondary and tertiary analysis softwares. Datasets such as human small RNA, whole transcriptome, E.coli single reads and PE reads can be found in that website. I got a chance to play around with SOLiD de novo assembly tool using E.coli dataset. The software is user friendly. I imagined working with color space is a very complicated task but it's easier than I expected. This software automatically display base read after assembly. There is a Find option to locate the reads which I find pretty useful. Another advantage is that the softwares can be installed on all types of OS (which is great for Windows user like me). Click here to read application note on SOLiD software suite.

Here's a list of other SOLiD softwares
• Academic and open source - Velvet, MAQ, SOCS, Bowtie, BFAST, SHRiMP, PASS
• commercial softwares - NextGENe, CLC Bio, ZOOM, Partek
(Most resources come from seqanswers.com and lh3)


Related posts:
SOLiD Bioinformatics Part I : Introduction
SOLiD Bioinformatics Part II: de novo assembly