Details of assemblies used to evaluate RSEM-EVAL
================================================

The parameters used to generate each assembly used in our assesment of
RSEM-EVAL are listed below. The "Axolotl?" column is "yes" if this
parameter set was used to generate the assemblies of the Axolotl data,
and "no" otherwise. The "SS?" column is "yes" if this parameter
set was used to assemble the strand-specific mouse and yeast reads, and
"no" if it was only used the assemble the strand-non-specific
simulated and real mouse reads (and possibly the axolotl reads).


Trinity
-------

Axolotl?  SS?   Parameters
yes       yes   (default)
yes       yes   --min_glue 1
yes       yes   --min_iso_ratio 0.01
yes       yes   --min_iso_ratio 0.1
yes       yes   --glue_factor 0.01
yes       yes   --glue_factor 0.1
yes       yes   --min_pct_read_mapping 1
yes       yes   --min_pct_read_mapping 5
yes       yes   --max_reads_per_graph 10000000
yes       yes   --max_reads_per_graph 50000000
yes       yes   --max_number_of_paths_per_node 1
yes       yes   --max_number_of_paths_per_node 100
yes       yes   --path_reinforcement_distance 1
yes       yes   --path_reinforcement_distance 37
yes       yes   --min_iso_ratio 0.01 --min_glue 1
yes       yes   --min_iso_ratio 0.1 --min_glue 1
yes       yes   --glue_factor 0.01 --min_glue 1
yes       yes   --glue_factor 0.01 --min_iso_ratio 0.01
yes       yes   --glue_factor 0.01 --min_iso_ratio 0.1
yes       yes   --glue_factor 0.1 --min_glue 1
yes       yes   --glue_factor 0.1 --min_iso_ratio 0.01
yes       yes   --glue_factor 0.1 --min_iso_ratio 0.1
yes       yes   --min_pct_read_mapping 1 --min_glue 1
yes       yes   --min_pct_read_mapping 1 --min_iso_ratio 0.01
yes       yes   --min_pct_read_mapping 1 --min_iso_ratio 0.1
yes       yes   --min_pct_read_mapping 1 --glue_factor 0.01
yes       yes   --min_pct_read_mapping 1 --glue_factor 0.1
yes       yes   --min_pct_read_mapping 5 --min_glue 1
yes       yes   --min_pct_read_mapping 5 --min_iso_ratio 0.01
yes       yes   --min_pct_read_mapping 5 --min_iso_ratio 0.1
yes       yes   --min_pct_read_mapping 5 --glue_factor 0.01
yes       yes   --min_pct_read_mapping 5 --glue_factor 0.1
yes       yes   --max_reads_per_graph 10000000 --min_glue 1
yes       yes   --max_reads_per_graph 10000000 --min_iso_ratio 0.01
yes       yes   --max_reads_per_graph 10000000 --min_iso_ratio 0.1
yes       yes   --max_reads_per_graph 10000000 --glue_factor 0.01
yes       yes   --max_reads_per_graph 10000000 --glue_factor 0.1
yes       yes   --max_reads_per_graph 10000000 --min_pct_read_mapping 1
yes       yes   --max_reads_per_graph 10000000 --min_pct_read_mapping 5
yes       yes   --max_reads_per_graph 50000000 --min_glue 1
yes       yes   --max_reads_per_graph 50000000 --min_iso_ratio 0.01
yes       yes   --max_reads_per_graph 50000000 --min_iso_ratio 0.1
yes       yes   --max_reads_per_graph 50000000 --glue_factor 0.01
yes       yes   --max_reads_per_graph 50000000 --glue_factor 0.1
yes       yes   --max_reads_per_graph 50000000 --min_pct_read_mapping 1
yes       yes   --max_reads_per_graph 50000000 --min_pct_read_mapping 5
yes       yes   --max_number_of_paths_per_node 1 --min_glue 1
yes       yes   --max_number_of_paths_per_node 1 --min_iso_ratio 0.01
yes       yes   --max_number_of_paths_per_node 1 --min_iso_ratio 0.1
yes       yes   --max_number_of_paths_per_node 1 --glue_factor 0.01
yes       yes   --max_number_of_paths_per_node 1 --glue_factor 0.1
yes       yes   --max_number_of_paths_per_node 1 --min_pct_read_mapping 1
yes       yes   --max_number_of_paths_per_node 1 --min_pct_read_mapping 5
yes       yes   --max_number_of_paths_per_node 1 --max_reads_per_graph 10000000
yes       yes   --max_number_of_paths_per_node 1 --max_reads_per_graph 50000000
yes       yes   --max_number_of_paths_per_node 100 --min_glue 1
yes       yes   --max_number_of_paths_per_node 100 --min_iso_ratio 0.01
yes       yes   --max_number_of_paths_per_node 100 --min_iso_ratio 0.1
yes       yes   --max_number_of_paths_per_node 100 --glue_factor 0.01
yes       yes   --max_number_of_paths_per_node 100 --glue_factor 0.1
yes       yes   --max_number_of_paths_per_node 100 --min_pct_read_mapping 1
yes       yes   --max_number_of_paths_per_node 100 --min_pct_read_mapping 5
yes       yes   --max_number_of_paths_per_node 100 --max_reads_per_graph 10000000
yes       yes   --max_number_of_paths_per_node 100 --max_reads_per_graph 50000000
yes       yes   --path_reinforcement_distance 1 --min_glue 1
yes       yes   --path_reinforcement_distance 1 --min_iso_ratio 0.01
yes       yes   --path_reinforcement_distance 1 --min_iso_ratio 0.1
yes       yes   --path_reinforcement_distance 1 --glue_factor 0.01
yes       yes   --path_reinforcement_distance 1 --glue_factor 0.1
yes       yes   --path_reinforcement_distance 1 --min_pct_read_mapping 1
yes       yes   --path_reinforcement_distance 1 --min_pct_read_mapping 5
yes       yes   --path_reinforcement_distance 1 --max_reads_per_graph 10000000
yes       yes   --path_reinforcement_distance 1 --max_reads_per_graph 50000000
yes       yes   --path_reinforcement_distance 1 --max_number_of_paths_per_node 1
yes       yes   --path_reinforcement_distance 1 --max_number_of_paths_per_node 100
yes       yes   --path_reinforcement_distance 37 --min_glue 1
yes       yes   --path_reinforcement_distance 37 --min_iso_ratio 0.01
yes       yes   --path_reinforcement_distance 37 --min_iso_ratio 0.1
yes       yes   --path_reinforcement_distance 37 --glue_factor 0.01
yes       yes   --path_reinforcement_distance 37 --glue_factor 0.1
yes       yes   --path_reinforcement_distance 37 --min_pct_read_mapping 1
yes       yes   --path_reinforcement_distance 37 --min_pct_read_mapping 5
yes       yes   --path_reinforcement_distance 37 --max_reads_per_graph 10000000
yes       yes   --path_reinforcement_distance 37 --max_reads_per_graph 50000000
yes       yes   --path_reinforcement_distance 37 --max_number_of_paths_per_node 1
yes       yes   --path_reinforcement_distance 37 --max_number_of_paths_per_node 100

Notes:
- Trinity version r2012-03-17 was used.


Oases
-----

Axolotl?  SS?   Velvet parameters               Oases parameters
yes       yes    (default)                       (default)
yes       yes    -cov_cutoff auto                (default)
yes       yes    -cov_cutoff 5                   (default)
yes       yes    -exp_cov auto                   (default)
yes       yes    -exp_cov 20                     (default)
yes       yes    (default)                       -cov_cutoff 0
yes       yes    (default)                       -cov_cutoff 10
yes       yes    (default)                       -edgeFractionCutoff 0.1
yes       yes    (default)                       -edgeFractionCutoff 0.5
yes       yes    (default)                       -degree_cutoff 1
yes       yes    (default)                       -degree_cutoff 10
yes       yes    (default)                       -min_pair_count 1
yes       yes    (default)                       -min_pair_count 10
no        yes    -exp_cov auto -cov_cutoff auto  (default)
no        yes    -exp_cov auto -cov_cutoff 5     (default)
no        yes    -exp_cov 20 -cov_cutoff auto    (default)
no        yes    -exp_cov 20 -cov_cutoff 5       (default)
no        yes    -cov_cutoff auto                -cov_cutoff 0
no        yes    -cov_cutoff 5                   -cov_cutoff 0
no        yes    -exp_cov auto                   -cov_cutoff 0
no        yes    -exp_cov 20                     -cov_cutoff 0
no        yes    -cov_cutoff auto                -cov_cutoff 10
no        yes    -cov_cutoff 5                   -cov_cutoff 10
no        yes    -exp_cov auto                   -cov_cutoff 10
no        yes    -exp_cov 20                     -cov_cutoff 10
no        yes    -cov_cutoff auto                -edgeFractionCutoff 0.1
no        yes    -cov_cutoff 5                   -edgeFractionCutoff 0.1
no        yes    -exp_cov auto                   -edgeFractionCutoff 0.1
no        yes    -exp_cov 20                     -edgeFractionCutoff 0.1
no        yes    (default)                       -edgeFractionCutoff 0.1 -cov_cutoff 0
no        yes    (default)                       -edgeFractionCutoff 0.1 -cov_cutoff 10
no        yes    -cov_cutoff auto                -edgeFractionCutoff 0.5
no        yes    -cov_cutoff 5                   -edgeFractionCutoff 0.5
no        yes    -exp_cov auto                   -edgeFractionCutoff 0.5
no        yes    -exp_cov 20                     -edgeFractionCutoff 0.5
no        yes    (default)                       -edgeFractionCutoff 0.5 -cov_cutoff 0
no        yes    (default)                       -edgeFractionCutoff 0.5 -cov_cutoff 10
no        yes    -cov_cutoff auto                -degree_cutoff 1
no        yes    -cov_cutoff 5                   -degree_cutoff 1
no        yes    -exp_cov auto                   -degree_cutoff 1
no        yes    -exp_cov 20                     -degree_cutoff 1
no        yes    (default)                       -degree_cutoff 1 -cov_cutoff 0
no        yes    (default)                       -degree_cutoff 1 -cov_cutoff 10
no        yes    (default)                       -degree_cutoff 1 -edgeFractionCutoff 0.1
no        yes    (default)                       -degree_cutoff 1 -edgeFractionCutoff 0.5
no        yes    -cov_cutoff auto                -degree_cutoff 10
no        yes    -cov_cutoff 5                   -degree_cutoff 10
no        yes    -exp_cov auto                   -degree_cutoff 10
no        yes    -exp_cov 20                     -degree_cutoff 10
no        yes    (default)                       -degree_cutoff 10 -cov_cutoff 0
no        yes    (default)                       -degree_cutoff 10 -cov_cutoff 10
no        yes    (default)                       -degree_cutoff 10 -edgeFractionCutoff 0.1
no        yes    (default)                       -degree_cutoff 10 -edgeFractionCutoff 0.5
no        yes    -cov_cutoff auto                -min_pair_count 1
no        yes    -cov_cutoff 5                   -min_pair_count 1
no        yes    -exp_cov auto                   -min_pair_count 1
no        yes    -exp_cov 20                     -min_pair_count 1
no        yes    (default)                       -min_pair_count 1 -cov_cutoff 0
no        yes    (default)                       -min_pair_count 1 -cov_cutoff 10
no        yes    (default)                       -min_pair_count 1 -edgeFractionCutoff 0.1
no        yes    (default)                       -min_pair_count 1 -edgeFractionCutoff 0.5
no        yes    (default)                       -min_pair_count 1 -degree_cutoff 1
no        yes    (default)                       -min_pair_count 1 -degree_cutoff 10
no        yes    -cov_cutoff auto                -min_pair_count 10
no        yes    -cov_cutoff 5                   -min_pair_count 10
no        yes    -exp_cov auto                   -min_pair_count 10
no        yes    -exp_cov 20                     -min_pair_count 10
no        yes    (default)                       -min_pair_count 10 -cov_cutoff 0
no        yes    (default)                       -min_pair_count 10 -cov_cutoff 10
no        yes    (default)                       -min_pair_count 10 -edgeFractionCutoff 0.1
no        yes    (default)                       -min_pair_count 10 -edgeFractionCutoff 0.5
no        yes    (default)                       -min_pair_count 10 -degree_cutoff 1
no        yes    (default)                       -min_pair_count 10 -degree_cutoff 10

Notes:
- Velvet version 1.2.07 was used.
- Oases version 0.2.08 was used.
- For all read sets, we first generated a number of Oases assemblies, 
  each based on a single k-mer size, described below, and second merged 
  them using Oases with k-mer size 27.
- For the axolotl read sets, we used k-mer sizes 41, 45, and 49 in the
  first step.
- For all other read sets, we used k-mer sizes 19, 21, 23, ..., 41 in the
  first step. These k-mer sizes were suggested by Marcel Schultz.


SOAPdenovo-Trans
----------------

Axolotl?  SS?   Parameters
yes       no     (default)
yes       no     -K 19
yes       no     -K 31
yes       no     -M 0
yes       no     -M 3
yes       no     -d 1
yes       no     -d 10
yes       no     -D 0
yes       no     -D 10
yes       no     -e 0
yes       no     -e 10
yes       no     -M 0 -K 19
yes       no     -M 0 -K 31
yes       no     -M 3 -K 19
yes       no     -M 3 -K 31
yes       no     -d 1 -K 19
yes       no     -d 1 -K 31
yes       no     -d 1 -M 0
yes       no     -d 1 -M 3
yes       no     -d 10 -K 19
yes       no     -d 10 -K 31
yes       no     -d 10 -M 0
yes       no     -d 10 -M 3
yes       no     -D 0 -K 19
yes       no     -D 0 -K 31
yes       no     -D 0 -M 0
yes       no     -D 0 -M 3
yes       no     -D 0 -d 1
yes       no     -D 0 -d 10
yes       no     -D 10 -K 19
yes       no     -D 10 -K 31
yes       no     -D 10 -M 0
yes       no     -D 10 -M 3
yes       no     -D 10 -d 1
yes       no     -D 10 -d 10
yes       no     -e 0 -K 19
yes       no     -e 0 -K 31
yes       no     -e 0 -M 0
yes       no     -e 0 -M 3
yes       no     -e 0 -d 1
yes       no     -e 0 -d 10
yes       no     -e 0 -D 0
yes       no     -e 0 -D 10
yes       no     -e 10 -K 19
yes       no     -e 10 -K 31
yes       no     -e 10 -M 0
yes       no     -e 10 -M 3
yes       no     -e 10 -d 1
yes       no     -e 10 -d 10
yes       no     -e 10 -D 0
yes       no     -e 10 -D 10

Notes:
- Soapdenovo-Trans version 1.01 was used.


Trans-ABySS
-----------

Axolotl?  SS?  Parameters
no        no   (default)

Notes:
- No Trans-ABySS assembly was made of the Axolotl reads. For the other
  read sets, only one Trans-ABySS assembly was made, with default
  settings.
- For each read set, first we generated a number of assemblies, each
  based on a single k-mer size, and second we merged them. The single
  k-mer sizes were 26, 28, 30, ..., 64. Island size was 151 was used.
- A customized version of Trans-ABySS version 1.3.2 was used. The 
  customization to Trans-ABySS consisted of a script provided by 
  Ka Ming Nip on the Trans-ABySS mailing list, to accomodate unpaired
  reads.
- ABySS version 1.3.3 was used.