Source
r/bioinformatics•
Twity

Comparing Different Contig Software

question

I am currently working with a few different (de novo paired end) grass reads that I need to contig. My reads started at 300 BP but after I trimmed them for quality most sit around the 150-200 BP mark. I have run a contig with ABySS but was wondering if you guys has any opinion on software? I have found a few different papers comparing different software, and am worried that my current contig is too conservative.

What is your experience with running multiple contigs with different programs on the same data set? Do you have any strong opinions on contig software? Do I need to run error correction after the contig? I am still pretty new to the bioinformatics world and really would appreciate any advice for de novo gene assembly.

Posted Mar 28, 2015, 1:01 AM UTC

78
Dr_Roboto•

What sequencing technology did you use to generate the reads and are they from DNA or RNA?

3
TwityOP•

It's an Illumina paired end DNA read. Do you need more information on exactly what Illumina did to decide on contig software?

1
otonsofun•

I've worked with PriceTI for years and found it to be the best assembler, especially for Illumina paired-end data. Feel free to send me any questions about command line arguments etc if you end up giving it a try.

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TwityOP•

I'll add it to the list and give it a shot (hopefully tomorrow) and let you know. Thanks for the help.

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anudeglory•

Spades, Ray, SGA, Platanus, Velvet, Minia

2
Dr_Drosophila•

We did some testing looking at different assemblers (we are metagenomic ) and now only use velvet as it's quicker and provided more reliable results,if you have lots of data normalise it using khmer first to reduce size also try different options such as various kmer sizes to see if you can improve your assembly

1
TwityOP•

Thanks, I have done a lot of experimenting with different khmer and minimum repeat size using ABySS. I will definitely give Velvet a try. Do you guys get any significant changes to your data when you change minimum repeat? How big of a factor is the speed? I have access to more then enough processing power/time for the amount of data I need to analyze.

1
Dr_Drosophila•

We allowed for the default repeat settings as changing didn't seem to make a difference.

0