git clone https://github.com/dereneaton/pyrad.git sample1 ACAGG sample2 ATTCA sample3 CGGCATA sample4 AAGAACA pyRAD -n ## 1. uses current as working directory ./ ## 1. uses current as working directory /home/user/RAD/ ## 1. uses set location as working directory ./raw/*.fastq ## 2. path to raw data files raw/*.fastq.gz ## 2. path to raw data files (gzipped) ./barcodes.txt ## 3. path to barcodes file mydata.barcodes ## 3. path to barcodes file vsearch ## 4. in systemPATH /user/bin/usearch7.0.1090_i86linux32 ## 4. full path usearch7.0.1090_i86linux32 ## 4. in system PATH muscle ## 5. path to call muscle muscle3.8.31_i86linux32 ## 5. path to muscle long name TGCAG ## 6. PstI cutsite overhang C|TGCAG CWGC,AATT ## 6. ddRAD example for apeKI, EcoRI 8 ## 7. N processors 5 ## 8. mindepth for base calls 4 ## 9. maxN: max number of Ns in reads .90 ## 10. clustering threshold rad ## 11. Datatype pairddrad ## 11. Datatype 4 ## 12. minCov 4 ## 13. maxSharedH. arabidopsis_c90d5m4p4 ## 14. output name prefix A ## 15. selects prefix subset of files outg1,outg2 ## 16. outgroup selector for step 7 sample3,sample4 ## 17. Exclude from step 7 ~/RAD/fastq/*.fastq ## 18. Sorted files @~/RAD/fastq/*.fastq ## 18. sorted and stripped files 1 ## 19. max barcode mismatches 33 ## 20. min Quality score step 2 0 ## 21. strictness of Q filter 0.0005,0.001 ## 22. E and H, respectively 5 ## 23. MaxN in consensus seqs 5 ## 24. MaxH in a consensus seq 1 ## 25. diploid filter max haplos=2 10 ## 26. max SNPs in a final locus 8,12 ## 26. max SNPs in 1st and 2nd pair read 3 ## 27. max indels in a within-sample cluster 3,10 ## 27. max within-sample, max for across-sample cluster 3,6,10,10 ## 27. max within_read1,within_read2,across_read1,across_read2 998877 ## 28. random number seed 1,1 ## 29. overhang/trim ends of locus a,n ## 30. outputs formats 1 ## 31. call majority base on low depth sites 0 ## 32. don't keep trimmed sequences 50 ## 32. keep trimmed longer than 50 ## 33. default max depth option 50000 ## 33. a set max depth 9999999999 ## 33. no max depth 2 ## 34. exclude singletons 5 ## 34. exclude reads occurring less than 5 times 1 ## 35. use hierarchical clustering 0 ## 36. turn off repeat masking 6 ## 37. N vsearch threads A 4 1A0,1B0,1C0,1D0 B 4 2* C 4 3* ln -s ~/pyrad_v.3.0/pyRAD pyRAD ~/pyrad_v.3.0/pyRAD -h pyRAD -h pyRAD -p params.txt pyRAD -p params.txt -s 1 pyRAD -p params.txt -s 234567 pyRAD -p params.txt -s 7 yourfilename_R1_001.fastq yourfilename_R2_001.fastq >A CCRACACAGAGGGCCAATAGACACGTAGCTCGAGATCTCACCGCCCCCGCGATCT >B CCRACACAGAGGGCCAATAGACACGTAGCTCGAGATCTCACCGCCCCCGCGATCT >C CCRACACAGAGGGCCAATAGACACGTAGCTCGAGATCTCACCGCCCCCGCGATCT >D CCRACACAGAGGGCCAATAGACACGTAGCTCGAGATCTCACCGCMCCCGCGATCT >E CCRACACAGAGGGCCAATAGACACGTAGCTCGAGATCTCAGCACCCCCGCGATCT >F CCAACACAGAGGGCCAATAGACACGTAGCTCGAGATCTCAGCAACCCCGCGATCT //%P * *-- | >A CGTACAATAGGATGCACCGTTCGTAAAGTTCTTGACGGTGGACCGAGAACTAGGT >B CGTACAATAGGATGCACCGTTCGTAAAGTTCTTGACGGTGGACCGAGAACTAGGT >C CGTACAATAGGATGCACCGTTCGTAAAGTTCTTGACGGTGGACCGAGAACTAGGT >D CGTACAATAGGATGCACCGTTCGTCAAGTTGTTGACGGTGGACCGAGAACTAGGT >D CGTACAATAGGATGCACCGTTCGTCAAGTTGTTGACGGTGGACCGAGAACTAGGT //%D - - | >A CGTACAATAGGATGCACCGTTCGTAAAGTTCTTGACGGTGGACCGAGAACTAGGT >B CGTACAATAGGATGCACCGTTCGTAAAGTTCTTGACGGTGGGACGGACGGACGGA >C CGTACAATAGGATGCACCGTTCGTAAAGTTCTTGACGGTGGGACGGACGGACGGA >D CGTACAATAGGATGCACCGTTCGTCAAGTTGTTGACGGTGGACCGAGAACTAGGT //%S - - ** ******* *| ... sample1.consens.gz sample2.consens.gz sample3.consens.gz sample4.consens.gz sample5.consens.gz sample6.consens.gz sample7.consens.gz sample8.consens.gz sample9.consens.gz A 4 sample1,sample2,sample3,sample4 B 2 sample5,sample6,sample7,sample8 C 1 sample9