Summary:

For CABOG, we used the following command:

runCA -d . -p asm –s runCA.spec *.frg

runCA.spec contains multiple parameters used by CA or CABOG during assembly. The following deviations from default parameters were used in the best assembly for each organism:

Staphylococcus aureus:

No deviations from runCA.spec

Rhodobacter sphaeroides:

doOverlapBasedTrimming = 0, unittiger = bog, bogBreakAtIntersections = 0, bogBadMateDepth = 1000, merylThreads = 20, merOverlapperThreads = 1, merOverlapperExtendConcurrency = 20, merOverlapperSeedConcurrency = 20, ovlThreads = 1, ovlConcurrency = 20, ovlCorrConcurrency = 20 , frgCorrThreads = 1, frgCorrConcurrency = 20, merylMemory = 12800, ovlStoreMemory = 24000, doExtendClearRanges = 0, cnsConcurrency = 20

Human Chromosome 14:

doOverlapTrimming = 0, unittiger = bog, merylThreads = 20, merOverlapperThreads = 1, merOverlapperExtendConcurrency = 20, merOverlapperSeedConcurrency = 20, ovlThreads = 1, ovlConcurrency = 20, ovlCorrConcurrency = 20, frgCorrThreads = 4, frgCorrConcurrency = 8, cnsConcurrency = 20, merylMemory = 12800, obtMerThreshold = 1000, ovlMerThreshold = 1000, ovlStoreMemory = 12800, frgCorrBatchSize = 2000000, merOverlapperExtendBatchSize = 2000000, merOverlapperSeedBatchSize = 2000000, ovlCorrBatchSize = 2000000, doExtendClearRanges = 1, ovlMemory = 8GM --hashload 0.8, ovlHashBlockSize = 2000000, ovlRefBlockSize = 32000000

Bombus impatiens:

doOverlapTrimming = 0, unittiger = bog, merylThreads = 24, merOverlapperThreads = 1, merOverlapperExtendConcurrency = 24, merOverlapperSeedConcurrency = 24, ovlThreads = 1, ovlConcurrency = 24, ovlCorrConcurrency = 24, frgCorrThreads = 4, frgCorrConcurrency = 8, cnsConcurrency = 24, merylMemory = 8192, obtMerThreshold = 1000, ovlMerThreshold = 1000, ovlStoreMemory = 8192, frgCorrBatchSize = 2000000, merOverlapperExtendBatchSize = 2000000, merOverlapperSeedBatchSize = 2000000, ovlCorrBatchSize = 2000000, doExtendClearRanges = 0, doFragmentCorrection = 0, ovlMemory = 8GM --hashload 0.8 --hashstrings 4000000, ovlHashBlockSize = 2000000, ovlRefBlockSize = 2000000