Usage¶

You can use refchooser to select a good reference from a list of assemblies. You will need either a directory of assemblies or a file containing the paths to the assemblies. Refchooser prints a table of metrics for each assembly.

The captured metrics are:

N50
N90
Number of contigs
Assembly length
Mean mash distance to all other assemblies

The results can be sorted by any metric you choose. By default, the assemblies are sorted by a simple score which is the N50/Distance ratio.

To print the table of assemblies sorted by N50:

# Choose the top 10 from a collection of 900 assemblies
refchooser metrics --sort N50 --top 10 assembly_paths.txt sketch_directory

Assembly   N50    N90    Contigs Length  Mean_Distance Path                    Score
SRR5868281 791291 119061 30      4845891 7.045173e-04  fasta/SRR5868281.fasta  1.123168e+09
SRR7439260 775386 146629 24      4815254 4.927176e-04  fasta/SRR7439260.fasta  1.573693e+09
SRR7906469 775033 432700 18      4779049 6.352714e-04  fasta/SRR7906469.fasta  1.220003e+09
SRR6949545 774499 146519 21      4814882 5.308503e-04  fasta/SRR6949545.fasta  1.458978e+09
SRR6949610 774132 105140 33      4888983 8.929775e-04  fasta/SRR6949610.fasta  8.669110e+08
SRR7426190 774120 146629 30      4820457 5.317999e-04  fasta/SRR7426190.fasta  1.455660e+09
SRR7426155 774120 146449 29      4775352 6.618484e-04  fasta/SRR7426155.fasta  1.169633e+09
SRR7441818 774120 146519 25      4797608 5.506614e-04  fasta/SRR7441818.fasta  1.405800e+09
SRR7439259 774120 146629 25      4815750 4.911346e-04  fasta/SRR7439259.fasta  1.576187e+09
SRR7439242 774120 146519 32      4803747 5.681594e-04  fasta/SRR7439242.fasta  1.362505e+09

To print the table of assemblies sorted by mean mash distance:

# Choose the top 10 from a collection of 900 assemblies
refchooser metrics --sort Mean_Distance --top 10 assembly_paths.txt sketch_directory

Assembly   N50    N90    Contigs Length  Mean_Distance Path                    Score
SRR1645597 226490 55522  55      4803421 4.611227e-04  fasta/SRR1645597.fasta  4.911708e+08
SRR1965968 237440 55508  59      4804728 4.614244e-04  fasta/SRR1965968.fasta  5.145805e+08
SRR1963305 166064 47353  61      4804588 4.618624e-04  fasta/SRR1963305.fasta  3.595530e+08
SRR1646405 226711 56774  58      4800826 4.629222e-04  fasta/SRR1646405.fasta  4.897389e+08
SRR1967694 287598 63327  54      4800251 4.637451e-04  fasta/SRR1967694.fasta  6.201639e+08
SRR7458586 216691 68846  48      4802064 4.642351e-04  fasta/SRR7458586.fasta  4.667700e+08
SRR7439539 333102 76943  45      4796679 4.646953e-04  fasta/SRR7439539.fasta  7.168180e+08
SRR5584738 216691 54594  62      4797573 4.649960e-04  fasta/SRR5584738.fasta  4.660061e+08
SRR7439240 774109 146629 34      4814374 4.658887e-04  fasta/SRR7439240.fasta  1.661575e+09
SRR8691682 216324 75764  47      4795530 4.659022e-04  fasta/SRR8691682.fasta  4.643121e+08

To print the table of assemblies sorted by the N50/Mean_Distance ratio score:

# Choose the top 10 from a collection of 900 assemblies
refchooser metrics --top 10 assembly_paths.txt sketch_directory

Assembly   N50    N90    Contigs Length  Mean_Distance Path                    Score
SRR7439240 774109 146629 34      4814374 4.658887e-04  fasta/SRR7439240.fasta  1.661575e+09
SRR7439252 774092 146519 26      4810069 4.722259e-04  fasta/SRR7439252.fasta  1.639241e+09
SRR5237981 749843 146968 30      4811975 4.681156e-04  fasta/SRR5237981.fasta  1.601833e+09
SRR7439259 774120 146629 25      4815750 4.911346e-04  fasta/SRR7439259.fasta  1.576187e+09
SRR7439260 775386 146629 24      4815254 4.927176e-04  fasta/SRR7439260.fasta  1.573693e+09
SRR7140222 773996 105140 27      4810707 4.939575e-04  fasta/SRR7140222.fasta  1.566928e+09
SRR7426191 774120 146629 28      4813941 5.066112e-04  fasta/SRR7426191.fasta  1.528036e+09
SRR7347002 774109 146519 34      4822419 5.137192e-04  fasta/SRR7347002.fasta  1.506872e+09
SRR1793292 774006 119046 56      4833765 5.247949e-04  fasta/SRR1793292.fasta  1.474873e+09
SRR6945020 774120 146519 21      4813673 5.303144e-04  fasta/SRR6945020.fasta  1.459738e+09