GuppyGermlineDNMs

Scripts for Lin, Y., Darolti, I., van der Bijl, W., Morris, J., Mank, J. E. (2023) Extensive variation in germline de novo mutations in Poecilia reticulata. Genome Research https://doi.org/10.1101/gr.277936.123

More detailed tutorial to be finished

1. Quality control for raw sequencing reads using FastQC and Trimmomatic

   python 01.QC_multi.py [-t THREADS] \
                        [-fq FASTQ_PATH] \
                        [-o OUTPUT] \
                        [-trim] \
                        [-qc]
   

2. Reference genome reconstruction based on Ensembl reference genome using LongRanger, LAST, ARCS and RagTag

   sh 02.refGenomeReconstruct.sh [seq] [ref]
   

3. Read alignment using BWA MEM.

   sh 03.alignment.sh [ref] [prefix]
   

4. Genotyping and SNP filtering

   #(1) Genotyping using BCFtools and GATK

   #(2) SNP filtering using SNPfiltering.py and BAMfilter.py

   sh 04.DNM.sh [father] [mother] [prefix] [ref]
   

5. Genotype phasing and Kinship analysis

   #(1) Genotype phasing using WhatsHap

   #(2) Kinship analysis using KING

   sh 05.phasingKinship.sh [fam] [ref]
   

6. Repeat identification using RepeatModeler2 and RepeatMasker

   sh 06.repeatAnnotation.sh [prefix] [output] [ref] [genomeSize]
   

7. Callable genome size calculation

   sh 07.CallableGenomeSize.sh [ref] [prefix]
   

8. Simulation using bamSurgeon.

   sh 08.simBamSurgeon.sh [ref] [prefix]