pacbioToCA

192221

pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=m120228_192221.fastq genomeSize=4650000 ../../tMiSeq_PE.frg

m120228_192221_42129_c100298890010000001523009207231260_s1_p0.fastq seqs amount:38542 seq avg len:2322.679985 total:89.52 Mb depth: 19.25X

(without genomeSize)PacBio_Illumia.fasta seqs amount:34981 seq avg len:2133.783826 total:74.64 Mb depth: 16.05X

4650000 viaMiseq.fasta seqs amount:34852 seq avg len:2130.841559 total:74.26 Mb depth: 15.97X => 看起來在只有一組的情況下，沒有差很多

210845

pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=m120228_210845.fastq genomeSize=4650000 ../../tMiSeq_PE.frg m120228_210845_42129_c000304152550000001500000112311370_s1_p0.fastq seqs amount:44794 seq avg len:2334.414140 total:104.57 Mb depth: 22.49X

(without genomeSize)PacBio_Illumia.fasta seqs amount:40666 seq avg len:2124.597010 total:86.40 Mb depth: 18.58X

4650000 viaMiseq.fasta seqs amount:40486 seq avg len:2120.237712 total:85.84 Mb depth: 18.46X => 看起來在只有一組的情況下，沒有差很多

Random Get Two

pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=Filtered_two.fastq genomeSize=4650000 ../tMiSeq_PE.frg Filtered_two.fastq seqs amount:77117 seq avg len:2184.208709 total:168.44 Mb depth: 36.22X

(without genomeSize)PacBio_Illumia.fasta seqs amount:63760 seq avg len:2199.845561 total:140.26 Mb depth: 30.16X

4650000 viaMiseq.fasta seqs amount:63411 seq avg len:2198.455315 total:139.41 Mb depth: 29.98X => 看起來在只有二組的情況下，沒有差很多

Random Get Three

pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=Filtered_three.fastq genomeSize=4650000 ../tMiSeq_PE.frg Filtered_three.fastq seqs amount:113284 seq avg len:2333.977711 total:264.40 Mb depth: 56.86X

PacBio_Illumia.fasta seqs amount:98165 seq avg len:2286.482249 total:224.45 Mb depth: 48.27X

4650000 viaMiseq.fasta seqs amount:70468 seq avg len:2815.903020 total:198.43 Mb depth: 42.67X => 看起來要有三組以上的的情況下，genomeSize才有效果。

Random Get Four

pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=Filtered_four.fastq genomeSize=4650000 ../tMiSeq_PE.frg Filtered_four.fastq seqs amount:136333 seq avg len:2386.664674 total:325.38 Mb depth: 69.97X

PacBio_Illumia.fasta seqs amount:118901 seq avg len:2320.548322 total:275.92 Mb depth: 59.34X

4650000 viaMiseq.fasta seqs amount:56298 seq avg len:3495.604515 total:196.80 Mb depth: 42.32X => 看起來要有三組以上的的情況下，genomeSize才有效果。

runCA

asm.spec used by us.

1

基本用法 runCA with asm.spec

   runCA -p asm -d asm -s asm.spec PBcR.viaMiseq.frg > asm.out 2>&1

2

web 提供，RunCA with parameters(Celera_Assembler_Parameters):

   runCA unitigger=bogart merSize=14 ovlMinLen=2000 utgErrorRate=0.015 utgGraphErrorRate=0.015 
   utgGraphErrorLimit=0 utgMergeErrorRate=0.03 utgMergeErrorLimit=0 -p asm -d asm asm.overCov.frg

3

Paper Script提供(asmCorrected.sh), RunCA with asm.spec and parameters： 照asmCorrected.sh上面的順序不會work，後來依照runCA 指令說明去放=> usage: runCA -d <dir> -p <prefix> [options] <frg> 就ok了。 並且使用wgs-package提供的asm.spec提供 D:\Boss Jade\201306\20130614_Hybrid assembly to_do_list\Filter_good_long_read\wgs-package\doc 但記得將grid 設0和 sge 關掉(mark掉)

   runCA -p asm -d asm -s asm.spec unitigger=bogart utgErrorRate=0.015 ovlMinLen=2000 ovlErrorRate=0.03 cgwErrorRate=0.10 cnsErrorRate=0.10 
   utgGraphErrorLimit=0 utgGraphErrorRate=0.015 utgMergeErrorLimit=0 utgMergeErrorRate=0.03 asm.overCov.frg