https://bioinformaticsonline.com/snippets/view/39755/palindrome-simulation-commands? https://bioinformaticsonline.com/snippets/view/39755/palindrome-simulation-commands Sun, 04 Aug 2019 19:24:42 -0500 https://bioinformaticsonline.com/snippets/view/39755/palindrome-simulation-commands (base) ➜ palindromeAssemblySim more allCommands 3315 mutate.sh in= mutant15CH101.fasta out=mutant153CH101.fasta id=97 3316 mutate.sh in=mutant15CH101.fasta out=mutant153CH101.fasta id=97 3317 history > allCommands 3318 cat ch101_read33155_template_pass_FAH31515.faa mutant3CH101.fasta mutant15CH101.fasta mutant153CH101.fasta > allPalindromeSimulated.fa 3319 ~/Tools/art_bin_MountRainier/art_illumina -ss MSv3 -sam -i allPalindromeSimulated.fa -p -l 251 -f 100 -m 300 -s 10 -o paired_dat 3320 ~/Tools/art_bin_MountRainier/art_illumina -ss MSv3 -sam -i allPalindromeSimulated.fa -p -l 250 -f 100 -m 300 -s 10 -o paired_dat 3321 ~/Tools/seqtk/seqtk mergepe paired_dat1.fq paired_dat2.fq > interleavedPE.fq 3322 ~/Tools/seqtk/seqtk seq -a interleavedPE.fq > interleavedPE.fasta 3323 ~/Tools/BWISE/Bwise.py -c 0 -p 4 -K 250 -t 10 -o simPalBwise -x interleavedPE.fasta 3326 cd masurca; ~/Tools/MaSuRCA-3.2.3/bin/masurca sim.conf 3327 ./assemble.sh 3328 cd .. 3329 ~/Tools/SPAdes-3.10.1-Linux/bin/spades.py --careful -1 paired_dat1.fq -2 paired_dat2.fq -o SpadesAssembly_OUT 3330 ~/Tools/platanus/platanus 3331 ~/Tools/platanus/platanus assemble 3332 ~/Tools/platanus/platanus assemble -o seePlatanus -f paired_dat[12].fq -t 10]]> Jit