> For the complete documentation index, see [llms.txt](https://cgps.gitbook.io/pathogenwatch/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/assembly-qc.md).

# Assembly QC

Thresholds define acceptable assembly quality ranges; genomes outside these bounds are flagged during QC.

## Bacteria

### *Acinetobacter baumannii* <a href="#id-470" id="id-470"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 17,000 bp |
| Contigs    | ≤ 490       |
| GC Content | 38–40%      |
| Length     | 3.6–4.6 Mbp |

Source: [Qualibact](https://qualibact.org/Acinetobacter/Acinetobacter_baumannii/)

### *Campylobacter coli* <a href="#id-195" id="id-195"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 25,000 bp |
| Contigs    | ≤ 180       |
| GC Content | 30–32%      |
| Length     | 1.6–2.2 Mbp |

Source: [Qualibact](https://qualibact.org/Campylobacter/Campylobacter_coli/)

### *Campylobacter jejuni* <a href="#id-197" id="id-197"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 22,000 bp |
| Contigs    | ≤ 160       |
| GC Content | 30–31%      |
| Length     | 1.5–2.0 Mbp |

Source: [Qualibact](https://qualibact.org/Campylobacter/Campylobacter_jejuni/)

### *Enterobacter cloacae* complex <a href="#id-354276" id="id-354276"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 41,000 bp |
| Contigs    | ≤ 420       |
| GC Content | 52–57%      |
| Length     | 4.6–5.8 Mbp |

Source: [Qualibact](https://qualibact.org/Enterobacter/Enterobacter_cloacae/)

### *Enterococcus faecium* <a href="#id-1352" id="id-1352"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 16,000 bp |
| Contigs    | ≤ 560       |
| GC Content | 37–39%      |
| Length     | 2.4–3.5 Mbp |

Source: [Qualibact](https://qualibact.org/Enterococcus/Enterococcus_faecium/)

### *Escherichia coli* <a href="#id-562" id="id-562"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 20,000 bp |
| Contigs    | ≤ 700       |
| GC Content | 50–52%      |
| Length     | 4.1–6.3 Mbp |

Source: [Qualibact](https://qualibact.org/Escherichia/Escherichia_coli/)

### *Haemophilus influenzae* <a href="#id-727" id="id-727"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 28,000 bp |
| Contigs    | ≤ 140       |
| GC Content | 37–39%      |
| Length     | 1.7–2.2 Mbp |

Source: [Qualibact](https://qualibact.org/Haemophilus/Haemophilus_influenzae/)

### *Klebsiella aerogenes* <a href="#id-548" id="id-548"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 75,000 bp |
| Contigs    | ≤ 200       |
| GC Content | 54–56%      |
| Length     | 4.9–6.0 Mbp |

Source: [Qualibact](https://qualibact.org/Klebsiella/Klebsiella_aerogenes/)

### *Klebsiella africana* <a href="#id-2489010" id="id-2489010"></a>

| Metric     | Range        |
| ---------- | ------------ |
| N50        | ≥ 281,000 bp |
| Contigs    | ≤ 60         |
| GC Content | 56–58%       |
| Length     | 5.2–5.4 Mbp  |

### *Klebsiella grimontii* <a href="#id-2058152" id="id-2058152"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 93,000 bp |
| Contigs    | ≤ 320       |
| GC Content | 54–57%      |
| Length     | 5.6–6.8 Mbp |

Source: [Qualibact](https://qualibact.org/Klebsiella/Klebsiella_grimontii/)

### *Klebsiella huaxiensis* <a href="#id-2153354" id="id-2153354"></a>

| Metric     | Range        |
| ---------- | ------------ |
| N50        | ≥ 176,000 bp |
| Contigs    | ≤ 80         |
| GC Content | 53–54%       |
| Length     | 6.2–6.4 Mbp  |

### *Klebsiella michiganensis* <a href="#id-1134687" id="id-1134687"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 55,000 bp |
| Contigs    | ≤ 380       |
| GC Content | 55–57%      |
| Length     | 5.7–7.0 Mbp |

Source: [Qualibact](https://qualibact.org/Klebsiella/Klebsiella_michiganensis/)

### *Klebsiella oxytoca* <a href="#id-571" id="id-571"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 68,000 bp |
| Contigs    | ≤ 350       |
| GC Content | 54–56%      |
| Length     | 5.3–6.8 Mbp |

Source: [Qualibact](https://qualibact.org/Klebsiella/Klebsiella_oxytoca/)

### *Klebsiella pasteurii* <a href="#id-2587529" id="id-2587529"></a>

| Metric     | Range        |
| ---------- | ------------ |
| N50        | ≥ 216,000 bp |
| Contigs    | ≤ 110        |
| GC Content | 54–56%       |
| Length     | 5.8–6.5 Mbp  |

### *Klebsiella pneumoniae* <a href="#id-573" id="id-573"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 54,000 bp |
| Contigs    | ≤ 390       |
| GC Content | 56–59%      |
| Length     | 4.9–6.4 Mbp |

Source: [Qualibact](https://qualibact.org/Klebsiella/Klebsiella_pneumoniae/)

### *Klebsiella quasipneumoniae* <a href="#id-1463165" id="id-1463165"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 48,000 bp |
| Contigs    | ≤ 400       |
| GC Content | 56–59%      |
| Length     | 4.5–6.3 Mbp |

Source: [Qualibact](https://qualibact.org/Klebsiella/Klebsiella_quasipneumoniae/)

### *Klebsiella quasivariicola* <a href="#id-2026240" id="id-2026240"></a>

| Metric     | Range        |
| ---------- | ------------ |
| N50        | ≥ 152,000 bp |
| Contigs    | ≤ 120        |
| GC Content | 56–57%       |
| Length     | 5.7–5.8 Mbp  |

### *Klebsiella spallanzanii* <a href="#id-2587528" id="id-2587528"></a>

| Metric     | Range        |
| ---------- | ------------ |
| N50        | ≥ 103,000 bp |
| Contigs    | ≤ 170        |
| GC Content | 53–54%       |
| Length     | 5.8–6.3 Mbp  |

### *Klebsiella variicola* <a href="#id-244366" id="id-244366"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 67,000 bp |
| Contigs    | ≤ 350       |
| GC Content | 56–58%      |
| Length     | 5.2–6.5 Mbp |

Source: [Qualibact](https://qualibact.org/Klebsiella/Klebsiella_variicola/)

### *Listeria monocytogenes* <a href="#id-1639" id="id-1639"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 66,000 bp |
| Contigs    | ≤ 120       |
| GC Content | 37–39%      |
| Length     | 2.8–3.3 Mbp |

Source: [Qualibact](https://qualibact.org/Listeria/Listeria_monocytogenes/)

### *Mycobacterium abscessus* <a href="#id-36809" id="id-36809"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 74,000 bp |
| Contigs    | ≤ 180       |
| GC Content | 63–65%      |
| Length     | 4.6–5.6 Mbp |

Source: [Qualibact](https://qualibact.org/Mycobacterium/Mycobacterium_abscessus/)

### *Mycobacterium tuberculosis* <a href="#id-1773" id="id-1773"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 34,000 bp |
| Contigs    | ≤ 320       |
| GC Content | 65–66%      |
| Length     | 4.2–4.6 Mbp |

Source: [Qualibact](https://qualibact.org/Mycobacterium/Mycobacterium_tuberculosis/)

### *Neisseria gonorrhoeae* <a href="#id-485" id="id-485"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 28,000 bp |
| Contigs    | ≤ 230       |
| GC Content | 52–53%      |
| Length     | 2.0–2.4 Mbp |

Source: [Qualibact](https://qualibact.org/Neisseria/Neisseria_gonorrhoeae/)

### *Neisseria meningitidis* <a href="#id-487" id="id-487"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 18,000 bp |
| Contigs    | ≤ 310       |
| GC Content | 51–53%      |
| Length     | 2.0–2.4 Mbp |

Source: [Qualibact](https://qualibact.org/Neisseria/Neisseria_meningitidis/)

### *Pseudomonas aeruginosa* <a href="#id-287" id="id-287"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 34,000 bp |
| Contigs    | ≤ 500       |
| GC Content | 65–67%      |
| Length     | 6.0–7.8 Mbp |

Source: [Qualibact](https://qualibact.org/Pseudomonas/Pseudomonas_aeruginosa/)

### *Renibacterium salmoninarum* <a href="#id-1646" id="id-1646"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 68,000 bp |
| Contigs    | ≤ 90        |
| GC Content | 56–57%      |
| Length     | 3.0–3.1 Mbp |

### *Salmonella enterica* <a href="#id-28901" id="id-28901"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 62,000 bp |
| Contigs    | ≤ 200       |
| GC Content | 51–53%      |
| Length     | 4.4–5.9 Mbp |

Source: [Qualibact](https://qualibact.org/Salmonella/Salmonella_enterica/)

### *Salmonella* Enteritidis <a href="#id-149539" id="id-149539"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 62,000 bp |
| Contigs    | ≤ 200       |
| GC Content | 51–53%      |
| Length     | 4.4–5.9 Mbp |

Source: [Qualibact](https://qualibact.org/Salmonella/Salmonella_enterica/)

### *Salmonella* Typhi <a href="#id-90370" id="id-90370"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 62,000 bp |
| Contigs    | ≤ 200       |
| GC Content | 51–53%      |
| Length     | 4.4–5.9 Mbp |

Source: [Qualibact](https://qualibact.org/Salmonella/Salmonella_enterica/)

### *Salmonella* Typhimurium <a href="#id-90371" id="id-90371"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 62,000 bp |
| Contigs    | ≤ 200       |
| GC Content | 51–53%      |
| Length     | 4.4–5.9 Mbp |

Source: [Qualibact](https://qualibact.org/Salmonella/Salmonella_enterica/)

### *Shigella flexneri* <a href="#id-623" id="id-623"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 20,000 bp |
| Contigs    | ≤ 700       |
| GC Content | 50–52%      |
| Length     | 4.1–6.3 Mbp |

Source: [Qualibact](https://qualibact.org/Escherichia/Escherichia_coli/)

### *Shigella sonnei* <a href="#id-624" id="id-624"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 20,000 bp |
| Contigs    | ≤ 700       |
| GC Content | 50–52%      |
| Length     | 4.1–6.3 Mbp |

Source: [Qualibact](https://qualibact.org/Escherichia/Escherichia_coli/)

### *Staphylococcus aureus* <a href="#id-1280" id="id-1280"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 26,000 bp |
| Contigs    | ≤ 280       |
| GC Content | 32–34%      |
| Length     | 2.6–3.3 Mbp |

Source: [Qualibact](https://qualibact.org/Staphylococcus/Staphylococcus_aureus/)

### *Streptococcus equi* <a href="#id-1336" id="id-1336"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 24,000 bp |
| Contigs    | ≤ 210       |
| GC Content | 40–42%      |
| Length     | 1.9–2.3 Mbp |

Source: [Qualibact](https://qualibact.org/Streptococcus/Streptococcus_equi/)

### *Streptococcus pneumoniae* <a href="#id-1313" id="id-1313"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 24,000 bp |
| Contigs    | ≤ 220       |
| GC Content | 39–40%      |
| Length     | 1.9–2.4 Mbp |

Source: [Qualibact](https://qualibact.org/Streptococcus/Streptococcus_pneumoniae/)

### *Vibrio cholerae* <a href="#id-666" id="id-666"></a>

| Metric     | Range       |
| ---------- | ----------- |
| N50        | ≥ 77,000 bp |
| Contigs    | ≤ 230       |
| GC Content | 47–48%      |
| Length     | 3.8–4.5 Mbp |

Source: [Qualibact](https://qualibact.org/Vibrio/Vibrio_cholerae/)

***

## Fungi

### *Candida auris* <a href="#id-498019" id="id-498019"></a>

| Metric     | Range         |
| ---------- | ------------- |
| N50        | ≥ 435,000 bp  |
| Contigs    | ≤ 110         |
| GC Content | 45–46%        |
| Length     | 12.0–12.4 Mbp |

***

## Viruses

### SARS-CoV-2 <a href="#id-2697049" id="id-2697049"></a>

| Metric       | Range            |
| ------------ | ---------------- |
| Contigs      | exactly 1        |
| GC Content   | 37.8–41.5%       |
| Length       | 27,000–30,500 bp |
| Ns / 100 kbp | ≤ 100            |

### Zika virus <a href="#id-64320" id="id-64320"></a>

| Metric       | Range            |
| ------------ | ---------------- |
| Contigs      | exactly 1        |
| GC Content   | 47–54%           |
| Length       | 10,300–11,000 bp |
| Ns / 100 kbp | ≤ 100            |