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Index of /release1/dpulex_jgi060905/genome-assembly-full-jazz_20060901

      Name                    Last modified       Size  Description

[DIR] Parent Directory 09-Apr-2019 09:22 - [TXT] info.txt 31-Aug-2006 22:51 1k [DIR] layout/ 19-Jul-2007 17:59 - [DIR] plots/ 19-Jul-2007 17:59 - [DIR] reference_sequence/ 19-Jul-2007 17:59 - [DIR] scaffolds/ 19-Jul-2007 17:59 - [DIR] unplaced_reads/ 19-Jul-2007 17:59 -

1. The 08/31/2006 build of Daphnia pulex was started on 08/12/2006
based on the following libraries:

3 kb:	 AZSH
8 kb:	 AZWY
40 kb:	 AZUX
8 kb:	 AZWZ
40 kb:	 AZUN
40 kb:	 AZSN
8 kb:	 AZXA


2. This data set contained a total of 2729325 reads, with the
following breakdown:

AZSN:	228191	= 8.4%
AZXA:	768	= 0.0%
AZUX:	768	= 0.0%
AZUN:	768	= 0.0%
AZWY:	768	= 0.0%
AZWZ:	1272122	= 46.6%
AZSH:	1225940	= 44.9%


3. Under the top-level assembly release directory the following
directories/files can be found:

1) readme - This file.

2) info - This file contains the assembly statistics for the main
genome scaffolds.

3) "scaffolds" subdirectory containing various scaffold information.

4) "unplaced_reads" subdirectory containing various unplaced read
information.

5) "plots" subdirectory containing various assembly supporting plots.

6) "layout" subdirectory containing various layout information
and ACE file.


More detailed info about the "scaffolds" subdirectory:

The initial assembly was further analyzed by its blast hits to
identify the main genome scaffolds.

1) "lists" subdirectory

a.) scaffold_analysis.txt - contains the notes on how the
scaffolds were classified from the initial BLAST results to the
revised set of contaminants and main genome scaffolds.

b.) The partitioned scaffold lists derived from the revised
BLAST results:

2) "sequences" subdirectory:

This directory contains the fasta sequence and quality files for the
above paritioned set of scaffolds.


3) "stats" subdirectory

a.) readme - file that contains the column information for the
scaffold statistics files.

b.) The scaffold statistics files for each of the paritioned
scaffold categories.

4) "blast_results" subdirectory - contains the megablast output files.

5) "blast_databases" subdirectory - contains BLAST nucleotide
databases for each of the scaffold fasta sequence files.

6) "ace" subdirectory - contains ace files that are created based on various
scaffold list files


The "unplaced_reads" subdirectory has the same directory structure of
information for the unplaced reads with the exception of the blast
results.