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levinas / assembly

Services to assemble genomes and metagenomes with user's choice of assembly algorithm. Currently supports single microbial genome assembly using velvet and/or kiki. More to come...
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test miseq pipeline on elm #2

Open levinas opened 10 years ago

levinas commented 10 years ago 
|  340   |   210   |            Stage 1/9: bhammer            | 0:02:26  |   b12.smart    |
|  341   |   210   |            Stage 2/4: spades             | 0:02:26  |    b12.fast    |
|  342   |   210   |            Stage 1/7: bhammer            | 0:00:30  |    b12.auto    |
|  343   |   210   |            Stage 1/4: velvet             | 0:00:00  |   b12.miseq    |

sal:/space2/fangfang/vbi/data/Brucella/2013-06-20/B12-0602S2_S7_L001_R1_001.fastq.gz sal:/space2/fangfang/vbi/data/Brucella/2013-06-20/B12-0602S2_S7_L001_R2_001.fastq.gz Reads are of uneven lengths.

@M00963:74:000000000-A3DM3:1:1101:15651:1404 1:N:0:7
GNCAGAAACAGGCCCACGAGATAGAAAACGCGCGCAATGCGGCGGCGCATACGGTGTTGGGCATTGCTCAAGGATTGGGCCATGACTACCACTCCGCTCCGATCTGCGTGCGCGCGGCGGCAAGCTTGCGGAAGAAAATGACGGTGAAGAGGATGGAGAGAAGGATCGCGACATAGGCCATGGCATTGGCAAGGCCCATCTGCGCATCCGAGTAGGCCGTGCGGCCCACGAGGGTCCAGATCAGCTCCGTG
+
A#>>AAAFFBCAF1EGGGGCGCFHGHHFHC?EGGCGGGFHCCG?EECGGGGHFGHHGGG/CAHHHHHFHGHHGHHHGGGHHGHGFHGHHHHFHHHGGGGGC@FGHHHCEFFCCCGG?AG?@;9EFFFF?@@?@BFFFFFFFFF@BAEBFFAEFFF?FFFFFFFFFFF??-@@@FFEFFFFFFFEFFFFEFBFEEE-BFFFFFE@@@F<FFF@9A9/BF?@?B@@;@@BF@-9>-BF-BFFFFFF/;F/AEE
@M00963:74:000000000-A3DM3:1:1101:16929:1411 1:N:0:7
GTTCCGACATCGACCTTCTTTTCCTGCTTCCCTATAAACAGACGCCCTGGGGCGAACAGGTTGTGGAATATACGCTCTACATGCTCTGGGACATGGGGCTGAAAGTCGGCCATTCCACCCGCAACATCGATGAGTGCATTCGTCTGGCGCGCGAGGACATGACCATTCGCACAGCCCTTCTCGATGCGCGCTTTCTTACCGGCGACAAGGATCTGTTCCGCACACTTGAAATCCGTTTCGAGGAGGAAAT
+
3A?3AAABBBFBFGGGGGGGGGFFFGGHHHHHHHHHHHHHHHHGEEGGHFEGGGGGGGHGHHHEEGGHHHHHHGGGGGGHHHGHGFGHHHHHGHFFHGGCDCHFH?GABGGGHGBGGGAGGCFGGGFHGGHHFHHHFHEFHHHGHGHG@ADGGGGCCGGGBBFGFGBBFGGGGFGFCFFFEFFBFF?>DDACFFBBBFFFFFFA>DFFFFFFFF/BFFF?DF;;.BFFFFF//9A9FB/AEF;;AD.FBF
levinas commented 10 years ago 
|  340   |   210   |           Complete with errors           | 3:16:25  |       b12.smart       |
|  341   |   210   |           Complete with errors           | 4:14:28  |        b12.fast       |
|  342   |   210   |           Complete with errors           | 2:51:16  |        b12.auto       |
|  343   |   210   |           Complete with errors           | 2:26:35  |       b12.miseq       |

340,342: ShortSequence: Sequence is too long. 341,343: Velvet does not support gz file