Index of /Datasets/Assemblathon/Assemblathon2/Additional_files

Icon  Name                    Last modified      Size  Description
[DIR] Parent Directory                             -   
[   ] Additional_file_9.xlsx  19-Jun-2013 18:03   22K  
[TXT] Additional_file_5.csv   22-Jan-2013 15:52   31K  
[   ] Additional_file_4.xlsx  22-Jan-2013 15:52  109K  
[   ] Additional_file_7.pdf   22-Jan-2013 15:52  117K  
[   ] Additional_file_3.pdf   22-Jan-2013 15:52  163K  
[   ] Additional_file_1.pdf   22-Jan-2013 15:52  169K  
[   ] Additional_file_6.pdf   22-Jan-2013 15:52  229K  
[   ] Additional_file_8.ta..> 28-Jan-2013 14:59  521K  
[   ] Additional_file_2.pdf   23-Jan-2013 15:35  3.6M  

README

This directory contain additional files to accompany the publication of the Assemblathon 2 paper (Bradnam et al., 2013)

Additional file 1
File format: PDF
Title: Supplementary Data Description
Description: Full details of the Illumina, Roche 454, and Pacific Biosciences sequencing data that were made available to participating teams.

Additional file 2
File format: PDF
Title: Supplementary Results
Description: Additional figures and tables to accompany the main text.

Additional file 3
File format: PDF
Title: Assembly Instructions
Description: Details provided by participating teams on how to use software to recreate their assemblies. All teams were asked to provide this information.

Additional file 4
File format: Microsoft Excel (.xlsx) spreadsheet
Title: Master spreadsheet containing all results
Description: Details of 102 different metrics for every assembly. First sheet contains a detailed README explaining all columns. Second sheet contains the data. Third sheet shows z-score values for 10 key metrics for all assemblies. Fourth sheet shows average rankings for all 10 key metrics.

Additional file 5
File format: comma-separated values (.csv)
Title: All results
Description: This file contains the same information as in sheet 2 of the master spreadsheet (Additional file 4), but in a format more suitable for parsing by computer scripts.

Additional file 6
File format: PDF
Title: Bird scaffolds mapped to bird Fosmids
Description: Results of using BLAST to align 46 assembled Fosmid sequences to bird scaffold sequences. Each figure represents an assembled Fosmid sequence with tracks showing read coverage, presence of repeats, and alignments to each assembly.

Additional file 7
File format: PDF
Title: Snake scaffolds mapped to snake Fosmids
Description: Results of using BLAST to align 24 assembled Fosmid sequences to snake scaffold sequences. Each figure represents an assembled Fosmid sequence with tracks showing read coverage, presence of repeats, and alignments to each assembly.

Additional file 8
File format: tarred, gzipped archive
Title: Bird and snake Validated Fosmid Region (VFR) data
Description: The validated regions of the bird and snake Fosmids are available as FASTA-formatted files, as are files that represent the 100 nt 'tag' sequences that were extracted from the VFRs.

Additional file 9
File format: Microsoft Excel (.xlsx) spreadsheet
Title: Details of all SRA/ENA/DDBJ accessions for input read data
Description: This spreadsheet contains identifiers for all Project, Study, Sample, Experiment, and Run accessions for bird, fish, and snake input read data