This is an old revision of the document!
====== assemblies/ ====== This directory has a subdirectory for each organism. ===== Pog/ ===== //Pyrobaculum oguniense// assemblies * newbler-assembly1/ is an attempt to do a de novo assembly using the 454 tools (Newbler) version 2.3, starting with the entire set of reads (including any contaminants). This resulted in 43 contigs and 2449932 bases. * newbler-clean1/ does not create an assembly, instead it is an attempt to remove contaminant reads from the Pog 454 data, by removing reads that map to //Helicobacter pylori// genomes. The results are in newbler-clean1/sff_cleaned/no_Hyp.sff * newbler-assembly2/ is a second de novo assembly using Newbler, starting from the cleaned reads of newbler-clean1/sff_cleaned/no_Hyp.sff ===== slug/ ===== * newbler-assembly1/ first attempt at de novo assembly using Newbler, using all the reads from 454_run1 and 454_run2.
