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Resequencing data and gap filling

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.

resequencing
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updated by Brice Sarver Brice Sarver • written by int11ap1 int11ap1

1 answer

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

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written by Brice Sarver Brice Sarver

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`

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written by int11ap1 int11ap1

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