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| Line 15: |
Line 15: |
|
| |
|
| * Formatting: | | * Formatting: |
| /fs/szdevel/dpuiu/SourceForge/wgs-assembler.030210/Linux-amd64/bin/fastqToCA \
| |
| -insertsize 3000 300 \
| |
| -libraryname 1 \
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| -type illumina \
| |
| -fastq /fs/szattic-asmg4/Bees/Bombus_impatiens/s_1_1_sequence.txt,/fs/szattic-asmg4/Bees/Bombus_impatiens/s_1_2_sequence.txt > 1.frg
| |
| =>
| |
| {LIB
| |
| act:A
| |
| acc:1
| |
| ori:I
| |
| mea:3000.000
| |
| std:300.000
| |
| src:
| |
| .
| |
| nft:10
| |
| fea:
| |
| forceBOGunitigger=1
| |
| isNotRandom=0
| |
| doNotTrustHomopolymerRuns=0
| |
| doRemoveDuplicateReads=0
| |
| doNotQVTrim=0
| |
| goodBadQVThreshold=0
| |
| doNotOverlapTrim=0
| |
| usePackedFragments=1
| |
| illuminaFastQType=illumina
| |
| illuminaSequence=/fs/szattic-asmg4/Bees/Bombus_impatiens/s_1_1_sequence.txt,/fs/szattic-asmg4/Bees/Bombus_impatiens/s_1_2_sequence.txt
| |
| .
| |
| }
| |
|
| |
| rm -fr asm.*
| |
| /fs/szdevel/dpuiu/SourceForge/wgs-assembler.030210/Linux-amd64/bin/gatekeeper \
| |
| -o /scratch1/Bombus_impatiens/Assembly/1.redo/./asm.gkpStore.BUILDING \
| |
| -T -F \
| |
| -E /scratch1/Bombus_impatiens/Assembly/1.redo/./asm.gkpStore.errorLog \
| |
| /scratch1/Bombus_impatiens/Assembly/1.redo/1.frg
| |
| => Segmentation fault
| |
|
| |
|
| = Assembly = | | = Assembly = |
Revision as of 19:42, 2 March 2010
Data
/fs/szattic-asmg4/Bees/Bombus_impatiens
- There are 7 pairs of data files (paired ends) : lanes 1..3,5..8 (lane 4 wasn't used)
1. Erroneous reads/bases, which we need to correct or discard
2. GC bias, so we can compute a-stats properly
3. Redundancy in the long paired ends, which are lane 1 and lane 2.
- Lane 1: 3Kbp insert; 34,944,099 reads
- Lane 3: 8Kbp insert; 32,540,640 reads
Assembly
/fs/szdevel/dpuiu/SourceForge/wgs-assembler.030210/Linux-amd64/bin/runCA