Next generation data analysis and assembly

[Mamoon Rashid]

Hi All,
Its just as introduction to me.
I am Mamoon, a newbie in NGS data analysis and assembly field. I am working as a Postdoc in King Abdullah University of Science and Technology. We have a good sequencing platforms here ranging from solexa to 454 to SOLID.
My first question is that how to choose one among these technologies for sequencing different organisms (like bacteria, eukaria etc.) and different samples (for e.g. genomic DNA, RNA).
Thanks

[michael_0214]

Hi, my Name is michael. I am working on the matter of next-geration sequence assembly for about one year. And two articles are recommended for your question:1. Assembly Algorithms for Next-generation Sequencing Data; 2. Comparing de novo assemblers for 454 transcriptome data.

[Mamoon Rashid]

Does anybody know how to identify uniquely mapped paired-end reads to the reference using BWA. Is this information exctracted after generating SAM file? please post with adequate details.
Thanks in anticipation

[wwq413]

To Mamoon Rashid,
yes, you need extract after SAM file.
below is what i used: I selected paired end reads with both ends mapped or one end mapped
awk '{if (($1 ~/^@/) || ($2 !=77) && ($2 !=141)) print}' $path/pe2.bwa.sam | samtools view -bT $path/superref.fasta - >$path/pe2.bwa.bam

I just used this method to publish a paper
Wang W, Messing J (2011) High-Throughput Sequencing of Three Lemnoideae (Duckweeds) Chloroplast Genomes from Total DNA. PLoS ONE 6(9):
e24670. doi:10.1371/journal.pone.0024670
You can have a quick review.