In our lab we have de novo assembled non-model plant WGS ( 1 paired-end library - 2x101 bp) of insert size 240 bp, with N50 around 1 kbp. The estimated genome size is around
2GB. Through read mapping we found coverage around 5x. I would like to get the idea to make possible of publication with this data.
I have some idea in mind to make use of this low coverage genome
1. Calling variant - finding SNP, heterozygosity & homozygosity (samtools, GATK)
2. Finding microsatellites (MISA etc)
3. Finding repeats using repeatmasker
4. Extracting and assembling mitochondria and chloroplast genome
Please add me if any ideas or related papers which can make of this low coverage genome.
2GB. Through read mapping we found coverage around 5x. I would like to get the idea to make possible of publication with this data.
I have some idea in mind to make use of this low coverage genome
1. Calling variant - finding SNP, heterozygosity & homozygosity (samtools, GATK)
2. Finding microsatellites (MISA etc)
3. Finding repeats using repeatmasker
4. Extracting and assembling mitochondria and chloroplast genome
Please add me if any ideas or related papers which can make of this low coverage genome.
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