================================================
The Opinionated Guide to Sequencing and Assembly
================================================

Authors: Holly Bik, C. Titus Brown, Nick Loman, Lex Nederbragt, and
Jared Simpson

Expiration date: 6/1/2014.

.. NOTE: source data for the table below is in opionated-guide.src, with
   script 'table-me.py' to produce the table below.

+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|                                **(Meta)genome** |                            **Goal** |                                                                                                                              **Dataset** |                                                                     **Assembly strategy** |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|                                        Bacteria |                   (Near) completion |                                                                                                                              PacBio 100x |                                                                               HGAP/Celera |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|                                        Bacteria |                   Draft few contigs |                                                                                 Ilmn Nextera/TruSeq PE 2x250 c50x + Nextera MP 5kbp c50x |                                                                               SPADES/MIRA |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|                                        Bacteria |       Draft 10s - 100(s) of contigs |                                                                                                        Ilmn Nextera/TruSeq PE 2x250 c50x |                                                                            SPADES/A5/MIRA |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|                   Small eukaryote up to 100 Mbp |                             contigs |                                                                                                        Ilmn Nextera/TruSeq PE 2x250 c50x |                                                                    SOAPdenovo, MIRA, SGA  |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|                   Small eukaryote up to 100 Mbp |                           scaffolds |                                                      Ilmn Nextera/TruSeq PE 2x250 c50x + Nextera MP 3-10kbp c50x (each) Optional: PacBio |               SOAPdenovo, MIRA, SGA (ALLPATHS_LG with right libraries) PBJelly and/or AHA |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|                           Eukaryote 100-500 Mbp |                             contigs |                                                                                                        Ilmn Nextera/TruSeq PE 2x250 c50x |                                                                           SOAPdenovo, SGA |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|                           Eukaryote 100-500 Mbp |                           scaffolds | Ilmn Nextera/TruSeq PE 2x250 MiSeq OR 2x150 HiSeq c50x; optional: multiple fr. lengths; Nextera MP 3-10kbp c50x (each); Optional: PacBio | SOAPdenovo, SGA, MaSuRCA, CA, Abyss (ALLPATHS_LG with right libraries) PBJelly and/or AHA |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|                             Eukaryotes over 500 | contigs / non-repetitive components |                                                                                   Ilmn Nextera/TruSeq PE 2x250 MiSeq OR 2x150 HiSeq c50x |                                                        SOAPdenovo, SGA, diginorm + velvet |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|                             Eukaryotes over 500 |                           scaffolds |                                                                                                as for 100-500 Mpb add more library types | SOAPdenovo, SGA, MaSuRCA, CA, Abyss (ALLPATHS_LG with right libraries) PBJelly and/or AHA |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|       Metagenome low diversity (2-50 "species") |    Diversity estimates, gene mining |                                                                                    Ilmn Nextera/TruSeq PE 2x150 HiSeq (tip: long insert) |                                                                     IDBA-UD, SPADES, MIRA |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|       Metagenome low diversity (2-50 "species") |                    Complete genomes |                                                                                                                       PacBio or Moleculo |                                                       IDBA-UD, diginorm + velvet/SGA, Ray |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|  Metagenome medium diversity (50-500 "species") |    Diversity estimates, gene mining |                                                                                    Ilmn Nextera/TruSeq PE 2x150 HiSeq (tip: long insert) |                                                       IDBA-UD, diginorm + velvet/SGA, Ray |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
| Metagenome high-diversity (e.g. soil, sediment) |    Diversity estimates, gene mining |                                                                                    Ilmn Nextera/TruSeq PE 2x150 HiSeq (tip: long insert) |                                                                     diginorm + velvet/SGA |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|                               Metatranscriptome |             Expression, gene mining |                                                                                                       Ilmn Nextera/TruSeq PE 2x150 HiSeq |                                                               diginorm + velvet/SGA, Ray? |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|                    Single-cell genome bacterial |                      Partial genome |                                                                                                        Ilmn Nextera/TruSeq PE 2x250 c50x |                                                                                    SPADES |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|          Single-cell genome eukaryote (protist) |                      Partial genome |                                                                                                        Ilmn Nextera/TruSeq PE 2x250 c50x |                                                           SPADES?, diginorm + velvet/SGA/ |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+
|                                         RNA-seq |               De novo transcriptome |                                               Ilmn TruSeq/Nextera PE 2x100 HiSeq. 50 - 100 million reads per tissue, 300-500 bp fragment |                                                                                   Trinity |
+-------------------------------------------------+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------+