| |
Abyss, Edena, SPAdes, SOAPdenovo2, Velvet, CISA (Note at: 20130718_MiSeq_with_verious_Assemblers) |
|
Abyss, Edena, SPAdes, SOAPdenovo2, Velvet, CISA (Note at: 20130718_MiSeq_with_verious_Assemblers) |
| |
MaSuRCA (note at: MaSuRCA for MiSeq Data) |
|
MaSuRCA (note at: MaSuRCA for MiSeq Data) |
| - |
= PacBio corrected reads (PBcR) =
|
|
|
| - |
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
|
|
|
| |
= Assemblies with hybrid methods = |
|
= Assemblies with hybrid methods = |
| - |
runCA (20130807_MG1655_s1s2_with_verious_Assemblers for 100X, 20120628_20120628_PacBio_With_CA(Celera Assembler)_Wgs), MIRA3
|
+ |
runCA (Details can be seen in [[Read Depths]], [[pacBioToCA]] and [[runCA]]), MIRA3
|
| |
== Hybrid assemble from pre-assembled contigs and long reads == |
|
== Hybrid assemble from pre-assembled contigs and long reads == |
