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jwcodee committed Aug 6, 2019
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Expand Up @@ -330,12 +330,11 @@ verbose logging enabled:
At the current time, the user must calculate suitable values for `B` and `H` on
their own, and finding the best value for `kc` may require experimentation
(optimal values are typically in the range of 2-4). Internally, the Bloom filter
assembler divides the memory budget (`B`) equally across (`kc` + 1) Bloom
filters, where `kc` Bloom filters are used for the cascading Bloom filter and
one additional Bloom filter is used to track k-mers that have previously been
included in contigs. Users are recommended to target a Bloom filter false
positive rate (FPR) that is less than 5%, as reported by the assembly log when
using the `v=-v` option (verbose level 1).
assembler allocates the entire memory budget (`B`) to a Counting Bloom filter,
and an additional (`B/8`) memory to another Bloom filter that is used to track
k-mers that have previously been included in contigs. Users are recommended to
target a Bloom filter false positive rate (FPR) that is less than 5%, as reported
by the assembly log when using the `v=-v` option (verbose level 1).

Assembling using a paired de Bruijn graph
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