To make sure you have selected a correct B value, There is no downside to using larger than necessary B value, except for A general guideline is:įor other genome sizes, the value for B can be interpolated. ( B/9) memory to another Bloom filter that is used to track k-mers that have previouslyĪ good value for B depends on a number of factors, but primarily on the The entire memory budget ( B * 8/9) to a Counting Bloom filter, and an additional Internally, the Bloom filter assembler allocates

If no unitsĪre specified bytes are assumed. With unit suffixes 'k' (kilobytes), 'M' (megabytes), 'G' (gigabytes). Reduce memory consumption by ten-fold compared to the MPI mode. The Bloom filter memory budget with the B parameter enables this mode, which can The recommended mode of running ABySS is the Bloom filter mode. If you have the Conda package manager (Linux, MacOS) installed, run: Installation Install ABySS using Conda (recommended) Assembling a strand-specific RNA-Seq library.Assembling using a paired de Bruijn graph.ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.

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