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Map Reads to a Reference Sequence


By: jmc


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 [1]. 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, with commit hash 3ddd7b87d41f89a404d95f083fb37c369f70d783.

Team members who deployed this App in KBase: John-Marc Chandonia. For questions, please contact us.

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Module Commit: 2c0fd8e0b7df5b9a564cd2e8deffd55c35ea1b4c