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mictadlo
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@mictadlo-10885
Last seen 4.9 years ago
Hello, We have one population consisted of 192 F3 lines resulting from a cross between two plant genomes.
All our GBS reads are stored in two folders (96 files in each).
1740-44-01> ls -1 *.gz
10_S0_L001_R1_001.fastq.gz
10_S0_L001_R2_001.fastq.gz
11_S0_L001_R1_001.fastq.gz
11_S0_L001_R2_001.fastq.gz
12_S0_L001_R1_001.fastq.gz
12_S0_L001_R2_001.fastq.gz
...
1740-44-02> ls -1 *.gz
10_S0_L001_R1_001.fastq.gz
10_S0_L001_R2_001.fastq.gz
11_S0_L001_R1_001.fastq.gz
11_S0_L001_R2_001.fastq.gz
12_S0_L001_R1_001.fastq.gz
12_S0_L001_R2_001.fastq.gz
...
I would like to generate genetic maps which contain linkage information between contigs, based on the co-segregation of specific markers on those contigs. The genetic map I would like to use to improve our assembly. I found the following tools:
- GenotypeR
- Genotype corrector
- BatchMap
- OneMap examples:
Do anyone know any complete examples from calling SNPs to the construction of genetic maps in order to improve the assembly?
Thank you in advance,
