BAM files and mapping
BESST requires sorted and indexed BAM files as input. Any read aligner + samtools can be used to obtain such files. Read pairs needs to be aligned in paired read mode. BESST provides a script (https://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py) for obtaining sorted and indexed BAM files with BWA-mem or BWA-sampe in one go. An example call for mapping with this script is
python reads_to_ctg_map.py /path/to/lib1_A.fq /path/to/lib1_B.fq /path/to/contigs.fasta --threads N
where N is an integer specifying how many threads BWA-mem should use. --nomem can be specified to the above call to use BWA-sampe as the paired read alignment pipeline.
https://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py
