Map short reads to a reference sequence with SAMtools
This method uses Burrows-Wheeler Aligner (BWA) to index a reference assembly, then align a set of short reads to it using the BWA-MEM algorithm . A Sequence/Alignment Map object should be created to store the result. However, because this object type is not yet available in KBase, this method creates a report on the mapping instead. The output BAM file can be downloaded from the report.
The mapping is done using
bwa mem CONTIGS_FILE READS_FILE | samtools view -S -b > BAM_FILE
The version of BWA-MEM used is from the Git repo at https://github.com/lh3/bwa.git, with commit hash 3ddd7b87d41f89a404d95f083fb37c369f70d783.
Team members who deployed this App in KBase: John-Marc Chandonia. For questions, please contact us.
-  Li H, Durbin R. Fast and accurate short read alignment with Burrows Wheeler transform. Bioinformatics. 2017. 25(14):1754 1760, doi:10.1093/bioinformatics/btp324 , https://academic.oup.com/bioinformatics/article/25/14/1754/225615
Module Commit: 2c0fd8e0b7df5b9a564cd2e8deffd55c35ea1b4c