Metagenomic Assembly Evaluation
Decreasing the assembler space
Ino de Bruijn / @inodb
Presentation at ino.pm/2014hack
de Bruijn Graph
- cut up reads into overlapping kmers
- unique kmers determine comp reqs
Purity noscaf recipes
Purity thresholds
Kmer origin
Impure contigs
- Number of kmers chimeric: 219020
- Number of kmers erroneous: 89314
- unclassifed: not in any of categories below
- a_tip_error: has erroneous kmers at the tip, but also other erroneous kmers
- one_tip_error: has one tip with erroneous_kmers and no other erroneous kmers
- two_tip_error: has two tips with erroneous_kmers and no other erroneous kmers
- one_break: has one point not located at the tips with only erroneous kmers
- 100% qrycov: the query contig is completely aligned to the reference
Predicting contig impurity
- Tried several assembly quality predictors without luck
- FRCurve
- REAPR
- ALE
Current State masmvaliweb
Current State masmvaliweb
Stop
