Hello,
We have sequenced genomic sequence of fruit crop through Hiseq 2000. The data are illumina paired-end fastq reads. The raw reads are filtered using trimmomatic with default settings and test with FastQC tool. After filteration, the total sequences are reduced from 505956290 to 418812062, with %GC 38 and sequence length is 101.It passed all test with warnings in per base sequence content and sequence duplication levels.
My single filtered fastq file size is 108Gbp and the genome size predicted through kmer genie and SGA preqc predicted to be around 2Gbp. The coverage is to be below 20x. Which genome assembler is good in assembling at low coverage?. What are the ways I can improve my genome assembly through computational approach?. Please let me know your suggestions and any pointer to journal papers which successed in assembling low coverage plant genome.
We have sequenced genomic sequence of fruit crop through Hiseq 2000. The data are illumina paired-end fastq reads. The raw reads are filtered using trimmomatic with default settings and test with FastQC tool. After filteration, the total sequences are reduced from 505956290 to 418812062, with %GC 38 and sequence length is 101.It passed all test with warnings in per base sequence content and sequence duplication levels.
My single filtered fastq file size is 108Gbp and the genome size predicted through kmer genie and SGA preqc predicted to be around 2Gbp. The coverage is to be below 20x. Which genome assembler is good in assembling at low coverage?. What are the ways I can improve my genome assembly through computational approach?. Please let me know your suggestions and any pointer to journal papers which successed in assembling low coverage plant genome.
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