Banana Slug Genomics

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Distributed construction of an FM index from multiple input files
jts edited this page on May 26, 2011 · 1 revision
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Distributed construction of an FM index from multiple input files
Example assembly workflow
FAQ
Indexing large data sets
Parameter tuning
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Scaffolding multiple libraries
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If your data sets consists of multiple files, you can construct the FM-index for each file separately then merge the indices together to obtain an index of the entire data. This requires much less memory than constructing an index from a single file containing the entire data set. For example, suppose your data consists of four files:

s_1_1.fastq 
s_1_2.fastq
s_2_1.fastq 
s_2_2.fastq
We begin by constructing an index of each file individually:

sga index s_1_1.fastq
sga index s_1_2.fastq
sga index s_2_1.fastq
sga index s_2_2.fastq
Then we want to merge the indices together in pairs until we obtain a single index:

sga merge -p merged1 s_1_1.fastq s_1_2.fastq
sga merge -p merged2 s_2_1.fastq s_2_2.fastq
sga merge -p final merged1.fa merged2.fa
The final index can then be used in other steps of the pipeline, for instance to error correct the original sequence files:

sga correct -p final s_1_1.fastq
sga correct -p final s_1_2.fastq
sga correct -p final s_2_1.fastq
sga correct -p final s_2_2.fastq
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