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Download Import Run
1: Bionano Data
output (cmap)
2: Estimated genome size - Parameter File
output (input)
3: Input GFA
output (gfa1)
4: Conflict resolution files
output (input)
5: Parse parameter value
Input file containing parameter to parse out of
integer_param (expression.json)
6: gfastats
Input file
SAK input file
output (fastq, fasta, fasta.gz, fastq.gz, gfa1, gfa1.gz)
7: Bionano Hybrid Scaffold
NGS FASTA
BioNano CMAP
Conflict resolution file
ngs_contigs_scaffold_trimmed (fasta)
hybridscaffolds_s1
ngs_contigs_not_scaffolded_trimmed (fasta)
non_hybridscaffolds_s1
report (txt)
s1_report
conflicts (txt)
s1_conflicts
results (zip)
s1_zip
Scaffolds: agp (agp)
s1_agp
8: gfastats
Input file
Input AGP file
Bionano scaffolds reconciliated: gfa (fastq, fasta, fasta.gz, fastq.gz, gfa1, gfa1.gz)
s1_gfa
9: gfastats
Input file
SAK input file
Bionano scaffolds reconciliated: fasta (fastq, fasta, fasta.gz, fastq.gz, gfa1, gfa1.gz)
s1_fasta
10: gfastats
Input file
Expected genome size
Assembly Statistics for s1 (tabular, text)
gfastats_asm_s1
#s1
11: gfastats
Input file
stats (tabular, text)
12: gfastats_data_prep
gfa_stats
gfastats data for plotting (input)
13: Cut
From
out_file1 (tabular)
14: Cut
From
out_file1 (tabular)
15: Scatterplot with ggplot2
Input in tabular format
Nx Plot (png)
Nx_plot
16: Scatterplot with ggplot2
Input in tabular format
Size Plot (png)
Size_plot
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