2223 canu -p 229e -d 229e genomeSize=27k maxInputCoverage=100 -nanopore ../229e.fastq
2224 canu -p 229e -d 229e genomeSize=27k maxInputCoverage=100 -nanopore ../229e.fastq useGrid=false
2225 ls
2226 ll
2227 cd 229e/
2228 ll
2229 less 229e.contigs.fasta
2230 cd ..
2231 conda install smartdenovo
2232 ls
2233 ll
2234 cd 229e/
2235 ll
2236 cd correction/
2237 ll
2238 ll 2-correction/
2239 ll 2-correction/results/
2240 ll 2-correction/
2241 cd .
2242 cd ..
2243 ls
2244 ll
2245 less 229e.report
2246 less 229e.unassembled.fasta
2247 cd ..
2248 ls
2249 ll
2250 mkdir canu_smartdenovo_pilon
2251 cd canu
2252 cd ..
2253 cd canu_smartdenovo_pilon/
2254 ls
2255 ll
2256 history |grep canu
2257 canu
2258 canu|grep corOut
2259 canu|grep corOutCoverage
2260*
2261 history |grep canu
2262 canu -p 229e -d 229e genomeSize=27k maxInputCoverage=100 -nanopore ../229e.fastq useGrid=false minOverlapLength=250
2263 ls
2264 ll
2265 cd 229e/
2266 ll
2267 canu
2268 canu -options
2269 ls
2270 ll
2271 cd ..
2272 rm -r 229e/
2273 rm -rf 229e/
2274 canu -correct -p 229e -d 229e genomeSize=27k maxInputCoverage=100 -nanopore ../229e.fastq useGrid=false minOverlapLength=250
2275 ls
2276 ll
2277 cd 229e/
2278 ll
2279 cd ..
2280 ll
2281 ls
2282 mkdir smartdenovo
2283 cd smartdenovo
2284 cp ../229e/229e.correctedReads.fasta.gz .
2285 ll
2286 gunzip 229e.correctedReads.fasta.gz
2287 ll
2288 smartdenovo.pl -c 1 229e.correctedReads.fasta > 229e.make
2289 ll
2290 make -f 229e.make
2291 ll
2292 gunzip wtasm.fa.gz
2293 ll
2294 less wtasm.fa
2295 cd ..
2296 mkdir nanopolish
2297 cd nanoplish
2298 cd nanopolish/
2299 nanopolish
2300 conda install nanopolish
2301 nanopolish index -d ../../../fast5/ -s ../../../nanopore_fastq/sequencing_summary.txt ../../../nanopore_fastq/229e.fastq
2302 ll
2303 ll ../../../nanopore_fastq/
2304 ll -lth ../../../nanopore_fastq/
2305 ls
2306 mv ../../../nanopore_fastq/229e.fastq.index.* .
2307 ll
2308 cp ../smartdenovo/wtasm.fa .
2309 cp ../../../nanopore_fastq/229e.fastq .
2310 ll
2311 mv wtasm.fa 229e_draft.fa
2312 ll
2313 bwa index 229e_draft.fa
2314 ll
2315 bwa mem -x ont2d -t 8 229e_draft.fa 229e.fastq | samtools sort -o reads.sorted.bam -T reads.tmp -
2316 ll
2317 samtools index reads.sorted.bam
2318 python3 nanopolish_makerange.py draft.fa | parallel --results nanopolish.results -P 8
2319 python3 nanopolish_makerange.py 229e_draft.fa | parallel --results nanopolish.results -P 8 nanopolish variants --consensus -o polished.{1}.vcf -w {1} -r 229e.fastq -b reads.sorted.bam -g 229e_draft.fa -t 4 --min-candidate-frequency 0.1
2320 which nanopolish_makerange.py
2321 python3 /home/bioinfo/miniconda2/envs/assembly/bin/nanopolish_makerange.py 229e_draft.fa | parallel --results nanopolish.results -P 8 nanopolish variants --consensus -o polished.{1}.vcf -w {1} -r 229e.fastq -b reads.sorted.bam -g 229e_draft.fa -t 4 --min-candidate-frequency 0.1
2322 ls
2323 ll
2324 rm .vcf
2325 ll
2326 cp 229e.fastq
2327 rm 229e.fastq*
2328 ll
2329 cp ../../../nanopore_fastq/229e.fasta .
2330 ll
2331 history |grep nanopolish
2332 nanopolish index -d ../../../fast5/ -s ../../../nanopore_fastq/sequencing_summary.txt ../../../nanopore_fastq/229e.fasta
2333 ll
2334 mv ../../../nanopore_fastq/229e.fasta.index* .
2335 ll
2336 python3 /home/bioinfo/miniconda2/envs/assembly/bin/nanopolish_makerange.py 229e_draft.fa | parallel --results nanopolish.results -P 8 nanopolish variants --consensus -o polished.{1}.vcf -w {1} -r 229e.fasta -b reads.sorted.bam -g 229e_draft.fa -t 4 --min-candidate-frequency 0.1
2337 ll
2338 ls
2339 nanopolish vcf2fasta -g 229e_draft.fa polished.*.vcf > polished_genome.fa
2340 ll
2341 ls
2342 ll -lth
2343 cd ..
2344 ll
2345 mkdir pilon
2346 cd pilon
2347 ll
2348 pilon
2349 history |grep bwa
2350 bwa mem ../nanopolish/229e_draft.fa ../../../illimina_6_samples/20210513_061525/Fastq/229E/229e_S5_L001_R1_001.fastq.gz ../../../illimina_6_samples/20210513_061525/Fastq/229E/229e_S5_L001_R2_001.fastq.gz | samtools sort -o 229e.draft.sorted.bam
2351 ll
2352 samtools index 229e.draft.sorted.bam
2353 ll
2354 pilon --genome ../nanopolish/polished_genome.fa --bam 229e.draft.sorted.bam
2355 pilon
2356 pilon --help
2357 which pilon
2358 ll /home/bioinfo/miniconda2/envs/assembly/bin/pilon
2359 java -Xmx 24G /home/bioinfo/miniconda2/envs/assembly/share/pilon-1.24-0/pilon.jar --genome ../nanopolish/polished_genome.fa --bam 229e.draft.sorted.bam
2360 java -Xmx24G /home/bioinfo/miniconda2/envs/assembly/share/pilon-1.24-0/pilon.jar --genome ../nanopolish/polished_genome.fa --bam 229e.draft.sorted.bam
2361 java -Xmx24G -jar /home/bioinfo/miniconda2/envs/assembly/share/pilon-1.24-0/pilon.jar --genome ../nanopolish/polished_genome.fa --bam 229e.draft.sorted.bam