Try `./popins4snake COMMAND --help' for more information on each command.
Try `./popins4snake COMMAND --help' for more information on each command.
```
```
Below we provide information on detailed explaination on each function comparing to the original PopIns2, how the program is constructed in the popinSnake workflow, and some customizable parameters to set up in the config files before running the workflow.
### The `crop-unmapped` function
### The `crop-unmapped` function
```
```
popins4snake crop-unmapped [OPTIONS] sample.bam
popins4snake crop-unmapped [OPTIONS] sample.bam
```
```
The crop-unmapped command identifies reads without high-quality alignment to the reference genome. The reads given in the input BAM file must be indexed, i.e. the file `sample.bam.bai` is expected to exist.
The crop-unmapped command identifies reads without high-quality alignment to the reference genome. The reads given in the input BAM file must be indexed, i.e. the file `sample.bam.bai` is expected to exist.
Originally part of the `assemble` function from PopIns and PopIns2, now an independent function for the workflow, the unmapped reads will be sorted by samtools, get filtered by read quality through SICKLE, and assembled.
crop-unmapped now provide its own quality filtering method by adding `--min-qual` and `--min-read-len`, but SICKLE can still be called directly from the workflow.
### The `merge-bams` function
**Workflow Configuration**\
```
Through the config file, user can select their desired quality filtering method and choose their preferred assembler: MINIA or VELVET following the quality filering step.
\[Default\] The merge command builds a colored and compacted de Bruijn Graph (ccdbg) of all contigs of all samples in a given source directory _DIR_.
The merge-contig command builds a colored and compacted de Bruijn Graph (ccdbg) of all contigs of all samples in a given source directory. For general usage see [PopIns2](https://github.com/kehrlab/PopIns2) merge function.
By default, the merge module finds all files of the pattern `<DIR>/*/assembly_final.contigs.fa`. To process the contigs of the [assemble command](#the-assemble-command) the __-r__ input parameter is recommended. Once the ccdbg is built, the merge module identifies paths in the graph and returns _supercontigs_.
**Workflow Configuration**\
As in the snakemake workflow, user can set the k-mer size for customized Algorithm options. The function also supports multi-threading for running on a cluster, setup the number of threads in cluster_config.yaml.
An alternative way of providing input for the merge command is to directly pass a ccdbg. Here, the merge command expects a _GFA_ file and a _bfg_colors_ file, which is specific to the Bifrost. If you choose to run the merge command with a _pre_-built GFA graph, mind that you have to set the Algorithm options accordingly (in particular __-k__).
As part of the contigmap function, `merge-bams` merges the mapped and sorted files from BWA and SAMtools in the contigmap module. This process anchors both ends of each read pair, ensuring that pairs with one end aligned to the reference genome and the other end aligned to the supercontigs are brought together.
