https://bioinformaticsonline.com/snippets/view/36933/mapping-with-bwa-mem-or-bwa-sampe-in-one-go-with-python-script? https://bioinformaticsonline.com/snippets/view/36933/mapping-with-bwa-mem-or-bwa-sampe-in-one-go-with-python-script Thu, 14 Jun 2018 06:37:37 -0500 https://bioinformaticsonline.com/snippets/view/36933/mapping-with-bwa-mem-or-bwa-sampe-in-one-go-with-python-script 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]]> Jit