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--- archive:bioinformatic_tools:jellyfish [2011/04/24 19:22]
eyliaw
+++ archive:bioinformatic_tools:jellyfish [2011/05/16 20:37]
karplus Added numbers from Illumina run 1 counts
@@ Line 1: / Line 1: @@
+====== Jellyfish ======
 Jellyfish is a tool for fast, memory efficient counting of K-mers in DNA [[http://www.cbcb.umd.edu/software/jellyfish/]][(cite:jellyfish>Marçais, Guillaume and Kingsford, Carl. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770 first published online January 7, 2011 doi:10.1093/bioinformatics/btr011)]
@@ Line 29: / Line 30: @@
 {{:bioinformatic_tools:slug-fit-gamma-illumina1.png|}}
+For run1, the first few distinct kmer with the specified multiplicities are
+  - 970,576,481 (19-mers)  1,242,303,036 (22-mers)
+  - 95,088,167 (19-mers)  100,246,200 (22-mers)
+  - 55,353,345 (19-mers)  67,039,962 (22-mers)
+  - 60,129,122 (19-mers)  77,381,432 (22-mers)
+Total distinct: 2,298,220,805 (19-mers) 2,699,479,169 (22-mers)
+These counts were done before running SeqPrep, so include adapter reads.
 ====== Gamma distribution is wrong ======

Banana Slug Genomics