Table 2

Jobs in the Pairwise alignment pipeline for Human-Pika

Analysis

Number of jobs

Granularity


ChunkAndGroupDna

4

2 per genome


CreatePairAlignerJobs

1

1 per pipeline


BlastZ-e1886dc

97920

As many as required


UpdateMaxAlignmentLengthBeforeFD

1

1 per pipeline


CreateFilterDuplicatesJobs

2

1 per genome


TargetFilterDuplicates-e1886dc

113

1 per human segment


QueryFilterDuplicates-e1886dc

193095

1 per pika segment


UpdateMaxAlignmentLengthAfterFD

1

1 per pipeline


DumpLargeNibForChains

2

1 per genome


CreateAlignmentChainsJobs

1

1 per pipeline


AlignmentChains-26aa1260

425698

As many as required


UpdateMaxAlignmentLengthAfterChain

1

1 per pipeline


CreateAlignmentNetsJobs

1

1 per pipeline


AlignmentNets-34de6ee1

5770

As many as required


UpdateMaxAlignmentLengthAfterNet

1

1 per pipeline


PairwiseHealthCheck

2

2 per pipeline


TOTAL

722613


This table shows the final number of jobs run for each analysis. The last column gives a short explanation on the number of jobs for each analysis. 113 human segments correspond to the 25 chromosomes (1 to 24, X, Y and MT) and an extra 88 supercontigs not yet assembled into chromosomes. The pika genome is scattered in 193095 segments. Both AlignmentChain and AlignmentNets jobs are defined by the CreateAlignmentChainJobs and CreateAlignmentNetsJobs jobs respectively.

Severin et al. BMC Bioinformatics 2010 11:240   doi:10.1186/1471-2105-11-240

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