Assembly Pipeline
- Inspect data
- Trim adapters
- Correct errors
- Merge reads
- Estimate k-mer abundance
- Assemble
- Scaffold
- Close gaps
- Polish
- Align to reference
- Calculate metrics
- Count core genes
- Generate reports
Inspect data
- Check library and sequencing quality
- Discard bad lanes
- Trim bad cycles
Trim adapters
Remove adapter sequence from reads
Correct errors
Reduce memory utilization and improve contiguity and correctness
Merge reads
- Merge overlapping reads
- Fill the gap between paired-end reads
Estimate k-mer abundance
- Estimate memory usage prior to assembly
- Pick a range of values for k to assemble
Assemble
Assemble reads into contigs
Scaffold
Join contigs into scaffolds
Close gaps
- Fill gaps of Ns with sequence
- Improve the contig N50
Polish
Identify and remove errors from the assembly
Align to reference
Identify misassemblies
Calculate metrics
for contiguity, correctness, completeness
Count core genes
Estimate assembly completeness without a reference
Generate reports
Generate tables and figures of
contiguity, correctness, completeness
