## Tools : `tl`

Run execute scripts

```{eval-rst}
.. module:: verkkofillet.tl
```

```{eval-rst}
.. currentmodule:: verkkofillet
```

### Graph Alignment
```{eval-rst}
.. autosummary::
   :nosignatures:
   :toctree: generated/

   tl.graphIdx
   tl.graphAlign

``` 

### QV check
```{eval-rst}
.. autosummary::
   :nosignatures:
   :toctree: generated/

   tl.mkMeryl
   tl.calQV

``` 

### Chromosome assignment and Contig QC
```{eval-rst}
.. autosummary::
   :nosignatures:
   :toctree: generated/

   tl.getT2T
   tl.rmrDNA
   tl.chrAssign
   tl.showPairwiseAlign
   tl.mapBetweenNodes

``` 

### Insert gaps
```{eval-rst}
.. autosummary::
   :nosignatures:
   :toctree: generated/

   tl.insertGap

``` 

### Modifying assembly
```{eval-rst}
.. autosummary::
   :nosignatures:
   :toctree: generated/

   tl.sortContig
   tl.renameContig
   tl.detect_internal_telomere
   tl.runTrimming
   tl.flipContig
   tl.convertRefName
   tl.filterContigs

```