---
# System prepended metadata

title: OLD F. cylindrus assembly

---

# OLD F. cylindrus assembly

# Initial graph and workspace

Graph at k=63, tipclipped at 125bp x3. Both GFAs dumped:

```python
%cd /Users/clavijob/fcyl_pe2/sdgdbg/
import SDGpython as SDG
from graphcleaning import *

K=63
MIN_CVG=2
NUM_BATCHES=8

ws=SDG.WorkSpace()
peds=ws.add_paired_reads_datastore('fcyl_pe2.prseq')
SDG.GraphMaker(ws.sdg).new_graph_from_paired_datastore(peds,K,MIN_CVG,NUM_BATCHES)
ws.sdg.write_to_gfa1("fcyl_pe2_k63c2.gfa")
simple_structures_stats(ws.sdg)
c=SDG.GraphContigger(ws)
c.clip_tips(125,3)
ws.sdg.write_to_gfa1("fcyl_pe2_k63c2_tc125x3.gfa")
simple_structures_stats(ws.sdg)
```

Graph reloaded, KCI and paired read mapping:

```python
%cd /Users/clavijob/fcyl_pe2/sdgdbg/
import SDGpython as SDG
from graphcleaning import *
from graphuntangling import *
from graphstriding import *

ws=SDG.WorkSpace()
ws.sdg.load_from_gfa("fcyl_pe2_k63c2_tc125x3.gfa")
ws.sdg.write_to_gfa1("fcyl_pe2_initial.gfa")

peds=ws.add_paired_reads_datastore('fcyl_pe2.prseq')
lords=ws.add_long_reads_datastore('fcyl_nano.loseq')

kc=ws.add_kmer_counter("main")
kc.add_count("pe",peds)
kc.set_kci_peak(61)
kc.compute_all_kcis()
print(ws.sdg.stats_by_kci())
ws.dump("fcyl_pe2_initial.sdgws")

peds.mapper.path_reads()
peds.mapper.dump_readpaths("fcyl_pe2_initial_readpaths.dump")
```

```python

```


|  KCI  |    Total bp   |   Nodes  |  Tips   |     N25    |     N50    |     N75    |
|-------|--------------:|---------:|--------:|-----------:|-----------:|-----------:|
| None  |      30272273 |   407162 |    9961 |         87 |         72 |         64 |
| < 0.5 |      29221328 |   210177 |    9995 |        125 |        125 |        125 |
| ~ 1   |      41232715 |   175140 |    1354 |        552 |        257 |        149 |
| ~ 2   |      35931827 |   169937 |     367 |        445 |        220 |        127 |
| ~ 3   |      16008585 |    82284 |      52 |        396 |        191 |        125 |
| > 3.5 |       2554306 |    15334 |      89 |        276 |        147 |        125 |
| **All**   |     155221034 |  1060034 |   21818 |        318 |        127 |        124 |


## Unused read coverage (idea).

Use 63-mers to start with. Only 63-mers of "unused" reads contribute to the coverage of a 63-mer (either on a KC or over the nodes, I am not sure). Once a read is "consumed" (i.e. it is fully assigned to a node), all the coverage of its constituen 63-mers is removed from the problem. Alternatively, a new DBG could be constructed by using only reads that are unused so far.
