tools for closing gaps and construct a complete chromosome in Galaxy

Question

[Bioinformática]

Hi everybody, I need some help. I am working on Galaxy in a new genome. I used the SPADEs tool for ensembling my sequences and it generated about 130.000 sequences.

My question is if there is some tool in Galaxy that decreases the number of gaps and gets contigs larger as chromosomes. I appreciate any help you can provide.

[Ram]

Please ask: https://help.galaxyproject.org/

[Ram]

This question has now been cross-posted to Galaxy Help: https://help.galaxyproject.org/t/tools-for-closing-gaps-and-construct-a-complete-chromosome-in-galaxy/11511

Answer 1

[colindaven]

You probably need long reads. 130,000 contigs is way too many to work with. What is your genome of interest ? How big is it ? What is your contig N50 ?

These days you can assemble complex ca 1 GB plant genomes in less that 100 contigs with long reads. I'd be loathe to work with any assembly with more than about 6000 contigs if I can avoid it.

If you can't generate a better assembly, perhaps scaffolding with a good and closely related genome is an option with a tool like Ragtag https://github.com/malonge/RagTag

[Bioinformática]

My genome is about 100Mb from a microalgae. There is a genome complete that I can use as a reference. The N50 is 6100. I only have Illumina reads 150 bp long. I can´t find any tool that reduces the number of contigs. I don´t know Ragtag, I´ll check it out. Thanks, colindaven!