If you want to compile from the source, you need to have the GCC compiler, GNU make
and zlib development files installed. Then type `make` in the source code
directory to compile.
### <a name="general"></a>General usage
Before mapping, an index of the reference needs to be created and saved on the disk:
```sh
chromap -r ref.fa -o index
```
The users can input the min fragment length expected in their sequencing experiments by **--min-frag-length**. Then Chromap will choose proper k-mer length and window size to build the index. For human genome, it only takes a few minutes to build the index.
Without any preset parameters, Chromap takes a reference database and a query sequence
file as input and produce approximate mapping, without base-level alignment in the [BED format][bed]:
```sh
chromap -x index -r ref.fa -1 query.fq -o approx-mapping.bed
```
You can ask Chromap to output alignments in the [SAM format][sam]:
```sh
chromap -x index -r ref.fa -1 query.fq --SAM-o alignment.sam
```
Chromap can take multiple input read files:
```sh
chromap -x index -r ref.fa -1 query1.fq,query2.fq,query3.fq --SAM-o alignment.sam
```
Chromap works with gzip'd FASTA and FASTQ formats as input. You don't need to convert between FASTA and FASTQ or decompress gzip'd files first.
***Importantly***, it should be noted that once you build the index, indexing
parameters such as **-k**, **-w** and **--min-frag-length** can't be changed during
mapping. If you are running Chromap for different data types, you will
probably need to keep multiple indexes generated with different parameters.
This makes Chromap different from BWA which always uses the same index
regardless of query data types.
### <a name="cases"></a>Use cases
To support different data types (e.g. ChIP-seq, Hi-C, ATAC-seq),
Chromap needs to be tuned for optimal performance and accuracy. It is usually
recommended to choose a preset with option **--preset**, which sets multiple
parameters at the same time.
#### <a name="map-chip"></a>Map ChIP-seq short reads
