Which assemblies of S.epidermidis_1585_5179_HD05 have been submitted to NCBI?

TODO: after annotation check if the app-gene has been truncated in 5179-R1. The 5179 generates 180 kDa and 220 kDa (isoforms) while 5179-R1 generated only a 140 kDa protein.

# See the paper: Induction of Staphylococcus epidermidis biofilm formation via proteolytic processing of the accumulation-associated protein by staphylococcal and host proteases

#------------ 5179 ------------
# -- from unicycler (5179_bold) --
    total         16       4   2,524,342   2,469,173         2,469,173
        1          1       1   2,469,173   2,469,173         2,469,173     complete
        2          1       1      17,749      17,749            17,749     complete
        3          1       0       4,761       4,761             4,761   incomplete
        4          1       1       4,595       4,595             4,595     complete -->
        5          1       0       3,735       3,735             3,735   incomplete
        6          1       0       3,718       3,718             3,718   incomplete
        7          1       0       3,573       3,573             3,573   incomplete
        8          1       1       2,449       2,449             2,449     complete -->
        9          1       0       2,411       2,411             2,411   incomplete
       10          1       0       2,371       2,371             2,371   incomplete
       11          1       0       2,365       2,365             2,365   incomplete
       12          1       0       1,637       1,637             1,637   incomplete
       13          1       0       1,568       1,568             1,568   incomplete
       14          1       0       1,505       1,505             1,505   incomplete
       15          1       0       1,403       1,403             1,403   incomplete
       16          1       0       1,329       1,329             1,329   incomplete

      1   2,469,173    1.00x   UniRef90_Q5HJZ9       1,901,872   reverse     100.0%     100.0%
      2      17,749    2.27x   UniRef90_A0A0H2VIR3       4,771   forward      93.2%      99.7%
      4       4,595   10.19x   none found (Submitted!)
      8       2,449   17.14x   none found (Submitted!)

# -- from trycycler (Submitted after adding the contig 4 and 8 since longer!) --
cluster_001_consensus   2471445 23      70      71  (Submitted!)
cluster_002_consensus   17749   23      70      71  (Submitted!)



#------------ 5179-R1 ------------
# -- from unicycler (5179R1_normal) --
Component   Segments   Links   Length      N50         Longest segment   Status
    total          2       2   2,486,311   2,468,563         2,468,563
        1          1       1   2,468,563   2,468,563         2,468,563   complete
        2          1       1      17,748      17,748            17,748   complete

# -- from trycycler --
cluster_001_consensus   2470004 23      70      71 (Submitted!)
cluster_002_consensus   17748   23      70      71 (Submitted!)
luster_003 with only one contig
luster_004 with only one contig
luster_005 with only one contig

#makeblastdb -in 5179_trycycler_chr.fasta -dbtype nucl
#blastn -db 5179_trycycler_chr.fasta -query 2-16.fasta -out 2-16_vs_trycycler_1.blastn -evalue 0.00000000001 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1


#------------ 1585 ------------

# 1585_normal/unicycler/chrom_plasmids.fasta
# -- from unicycler (1585_normal) --
Segment   Length      Depth    Starting gene     Position    Strand    Identity   Coverage
      1   2,443,574    1.00x   UniRef90_Q5HJZ9   1,085,369   forward      99.3%     100.0%
      2       9,014    3.72x   none found
      7       2,344   11.44x   none found
      8       2,255    9.81x   none found
# after correction using polypolish and polca (see ~/DATA/Data_Holger_S.epidermidis_1585_5179_HD05/1585_normal/unicycler)
1       2443600 3       70      71 (Submitted!)
2       9014    2478515 70      71 (Submitted!)
7       2344    2487661 70      71 (Submitted!)
8       2255    2490042 70      71 (Submitted!)

# -- from trycycler --
cluster_001_consensus   2443176 23      70      71
cluster_002_consensus   9014    23      70      71
cluster_003_consensus   2255    23      70      71
cluster_004_consensus   2344    23      70      71

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