
## Assembly statistics

`rule assembly_stats`


```{r assembly_stats, echo = F, message = F, warning = F, error = T}





#assembly_stats_df = read_tsv(glob$assembly_stats) 
assembly_stats_df = read_tsv(glob_list$assembly_stats) 
        

metadata_translate %>%
    select(sample, file_long) %>%
    left_join(assembly_stats_df, by = c("file_long" = "filename")) %>%
    select(sample, everything(), -file_long, -N50n, -N70, -N70n, -N90n) %>%
    custom_dt("assembly_stats", dom = "Blfrtip")


```

*Table `r tableno()`: Assembly statistics is provided by [assembly-stats](https://github.com/sanger-pathogens/assembly-stats#assembly-stats). N50 indicates the length of the smallest contig that (together with the longer contigs) covers at least half of the genome.*

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