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refMapper

Overview

refMapper aligns multiple assemblies against a single reference assembly, using lastal and lastdb from the LAST package (version 5.88).

The refMapper pipeline is usually invoked as part of a workflow to create a SNP tree.

refMapper is currently in version 1.0.

Summary of pipeline

refMapper prepares the reference assembly sequence for subsequent comparison with the other assemblies by running lastdb. Then a multithreaded job is started with a number of alignments consisting of pairwise comparisons of the other assemblies, each with the reference assembly. The alignments are carried out by the program lastal from the LAST package. (These are multiple sequence alignments since each assembly in these pairwise comparisons may consist of a number of sequences from its contigs.) The alignments are subsequently parsed and interpreted in order to identify mutations and also regions that successfully align with the reference, repetitive regions and regions with uncertain base calling or ambiguous alignment. The result is written out in GFF format for each assembly aligned to the reference.