Resequencing data and gap filling

Question

[int11ap1]

I have a reference genome with Ns and resequencing data. Is there some tool to fill these gaps with my resequencing data?

Thank you very much,

Andreu.

Answer 1

[Brice Sarver]

Some colleagues have tried GapFiller. They've had some success filling in gapped scaffolds using it.

[int11ap1]

I am running this command in a machine with 32gb RAM. It throws Segmentation fault error... `GapFiller --query genome.fasta --seed1 ../../Mapping_Data/fastq/unmapped_read-mapped-unmapped-mate_1.fastq --seed2 ../../Mapping_Data/fastq/unmapped_read-mapped-unmapped-mate_2.fastq --seed-ins 420 --seed-var 400`