README


This directory contains the Bombus impatiens data and assemblies presented in the GAGE paper.

Files & directories:
* Data.original/:	original Illumina reads (multiple files)
* Data.original.tgz:    original Illumina reads (compressed)
* Data.quakeCor.tgz:    quake corrected reads (compressed)
* Assembly.tgz:         assemblies (compressed)
* md5sum.txt:           the MD5 sums for the compressed files

To uncompress the files use the following Linux command:
  tar -xzvf *.tgz

Notes: 
* The following adapters are present in the original jumping reads 
    fwd_adapter             GATCGGAAGAGCGGTTCAGCAGGAATGCCGA
    rev_adapter             CGGCATTCCTGCTGAACCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
    circularization_adapter CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA
  The reads aligned to adapters and their mates have been removed from the original data set before read correction.
  The nucmer aligner was used to align the reads. The command line and paramteres used were:
    nucmer -l 8 -c 16 -b 32 -g 32