Mapsembler2 is a targeted assembly software. It takes as input any number of NGS raw read set(s) (fasta or fastq, gzipped or not) and a set of input sequences (starters). For each starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice. Mapsembler2 may be used for (not limited to): · Validate an assembled sequence (input as starter), e.g. from a de Bruijn graph assembly where read-coherence was not enforced. Checks if a known enzyme is present in a metagenomic NGS read set. · Enrich unmappable reads by extending them, possibly making them mappable · Checks what happens at the extremities of a contig · Check the presence / absence and quantify RNA seq splicing events. Check the presence/absence of SNPs or structural variants, …
Peterlongo, P., & Chikhi, R. (2012). Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. BMC bioinformatics, 13(1), 48.