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Paired reads are available at Illumina Miseq (Mate1, Mate2)
Read length: 151bp
Read amount: 5,729,470 X2
Insert size ~ 300bp
We combined MiSeq_Ecoli_MG1655_110721_PF_R1.fastq and MiSeq_Ecoli_MG1655_110721_PF_R2.fastq to MiSeq_PE.fastq.
The data in frg format were downloaded from Miseq100X
We have trimmed the sequence reads to be of error probability less than 0.05. The paired-end reads were discarded if one read is shorter than 150bp.
We therefore obtained 1,839,935 paired-end reads (~118X) with high quality for further analysis.
java convertFastqToFastaAndQual MiSeq_PE.fastq MiSeq_PE.fna MiSeq_PE.qual convert-fasta-to-v2.pl -mean 214 -stddev 21 -m Mate_info -l Illumia_Ecoli -s Ecoli_MG1655_PE.fna -q Ecoli_MG1655_PE.qual > Ecoli_MG1655_PE.frg
1 SMRT Cell of 10 kbp continuous long reads (CLR) for Escherichia coli K12 MG1655 were downloaded from this link.
The file of PacBio_10kb_CLR.fastq contains ~21X of E. coli CLR reads from a 10kb library that was filtered using standard PacBio filtering thresholds (minimum RQ=0.75, RL=50bp) (ref).
Abyss, Edena, SPAdes, SOAPdenovo2, Velvet, CISA (Note at: 20130807_MG1655_s1s2_with_verious_Assemblers) MaSuRCA (note at: MaSuRCA assembler)
To correct the PacBio CLR with raw short reads:
pacBioToCA -length 1000 -partitions 200 -l PacBio_Illumia -s pacbio.spec -fastq PacBio_10kb_CLR.fastq Ecoli_MG1655_PE.frg 1>PacBio_Illumia_Ecoli.out 2>error.out
To correct the PacBio CLR with 100X high-quality reads (p<0.05, length of paired-end read>=100bp)
pacBioToCA -length 500 -partitions 200 -l PacBio_Illumia -s pacbio.spec -fastq PacBio_10kb_CLR.fastq 100X_Ecoli_PE.frg
runCA (20130807_MG1655_s1s2_with_verious_Assemblers for 100X, 20120628_20120628_PacBio_With_CA(Celera Assembler)_Wgs), MIRA3
AHA, PBJelly, Cerulean, Patch