Any experience with scaffolding using SSPACE tool

Question

[seta]

Hi all,

I made de novo transcriptome assembly using about 300 millions PE reads (100bp from Illumina) with different k-mers. Several assembled transcriptome was merged and exposed to CAP3. Then, I used SSPACE-standard tool (version 3) to generate scaffold using the command perl SSPACE_Standard_v3.0.pl -l libraries.txt -s file1.fasta -k 5 -a 0.7 -m 50 -x 1 -T 3 -b output1. However, it sounds that scaffolding did not significantly improve the assembly. Actually, the number of initial contigs and scaffold were about 87000 and 85000, respectively. Similarly, N50 was 960 bp and 980 bp before and after scaffolding, respectively. It will be great if you share me any opinion or experience about it. How to improve more scaffolding step?

Thanks

Answer 1

[mapleforest]

In my opinion, SSPACE will not help your project in this case.

You need 1kb, 2kb, 3kb ... 20kb mate-pair libraries.

And I do not remember SSPACE can work on transcriptome assembly

[seta]

Thanks for your reply, however well working just on mate-pair library has not been mentioned in the tool's manual. Could you please let me know if you know any appropriate tool for scaffolding on transcriptome assembly?

[Bioinfo]

Hello , please how did you obtain the libraries file ?