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EnteroBase Backend Pipeline Optional Genera Assembly Criteria
- EnteroBase Backend Pipeline Optional Genera Assembly Criteria
- Assembly criteria for Listeria
- Assembly criteria for Clostridioides
- Assembly criteria for Klebsiella
- Assembly criteria for Photorhabdus
- Assembly criteria for Helicobacter
- Assembly criteria for Vibrio
- Assembly criteria for Mycobacterium
- Assembly criteria for Neisseria
- Assembly criteria for Peptoclostridium
- Assembly criteria for Clostridium
- Default assembly criteria
Assembly criteria for Listeria
| Metrics | Criteria |
|---|---|
| Number of bases | 2.5 Mbp – 3.3 Mbp |
| N50 value | >20kb |
| Number of contigs | <600 |
| Proportion of scaffolding placeholders (N’s) | <3% |
| Species assignment using Kraken | >70% contigs |
Assembly criteria for Clostridioides
| Metrics | Criteria |
|---|---|
| Number of bases | 3.6 Mbp – 4.8 Mbp |
| N50 value | 20kb |
| Number of contigs | <600 |
| Proportion of scaffolding placeholders (N’s) | <3% |
| Species assignment using Kraken | >65% contigs |
Assembly criteria for Klebsiella
| Metrics | Criteria |
|---|---|
| Number of bases | 4.3 Mbp – 7.3 Mbp |
| N50 value | >20kb |
| Number of contigs | <600 |
| Proportion of scaffolding placeholders (N’s) | <3% |
| Species assignment using Kraken | >65% contigs |
Assembly criteria for Photorhabdus
| Metrics | Criteria |
|---|---|
| Number of bases | 4 Mbp – 6 Mbp |
| N50 value | >20kb |
| Number of contigs | <700 |
| Proportion of scaffolding placeholders (N’s) | <3% |
| Species assignment using Kraken | >65% contigs |
Assembly criteria for Helicobacter
| Metrics | Criteria |
|---|---|
| Number of bases | 1.3 Mbp – 3 Mbp |
| N50 value | >20kb |
| Number of contigs | <300 |
| Proportion of scaffolding placeholders (N’s) | <3% |
| Species assignment using Kraken | >65% contigs |
Assembly criteria for Vibrio
| Metrics | Criteria |
|---|---|
| Number of bases | 3 Mbp – 5.3 Mbp |
| N50 value | >20kb |
| Number of contigs | <700 |
| Proportion of scaffolding placeholders (N’s) | <3% |
| Species assignment using Kraken | >65% contigs |
Assembly criteria for Mycobacterium
| Metrics | Criteria |
|---|---|
| Number of bases | 2.8 Mbp – 5.5 Mbp |
| N50 value | >15kb |
| Number of contigs | <600 |
| Proportion of scaffolding placeholders (N’s) | <3% |
| Species assignment using Kraken | >70% contigs |
Assembly criteria for Neisseria
| Metrics | Criteria |
|---|---|
| Number of bases | 1.8 Mbp – 2.4 Mbp |
| N50 value | >20kb |
| Number of contigs | <500 |
| Proportion of scaffolding placeholders (N’s) | <3% |
| Species assignment using Kraken | >65% contigs |
Assembly criteria for Peptoclostridium
| Metrics | Criteria |
|---|---|
| Number of bases | 2.5 Mbp – 4.8 Mbp |
| N50 value | >20kb |
| Number of contigs | <600 |
| Proportion of scaffolding placeholders (N’s) | <3% |
| Species assignment using Kraken | >65% contigs |
Assembly criteria for Clostridium
| Metrics | Criteria |
|---|---|
| Number of bases | 2 Mbp – 7 Mbp |
| N50 value | >20kb |
| Number of contigs | <800 |
| Proportion of scaffolding placeholders (N’s) | <3% |
| Species assignment using Kraken | >65% contigs |
Default assembly criteria
| Metrics | Criteria |
|---|---|
| Number of bases | 4 Mbp – 5.8 Mbp |
| N50 value | >20kb |
| Number of contigs | <600 |
| Proportion of scaffolding placeholders (N’s) | <3% |
| Species assignment using Kraken | >70% contigs |
Updated