I'm please to introduce the Mapsembler2 tool.
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, …
Based on the Minia data-structure it has a tiny memory footprint (human read sets can be analyzed with no more than 6GB memory) while being faster than other mentioned tools.
Finally we put effort to make it simple. The micro assembly step is in command-line fashion. We made it as simple as possible as shown in our dedicated video. Another video presents the graphical interface usage.
Home web page (download, GNU Affero General Public License, manual, galaxy install, videos) is here: http://colibread.inria.fr/mapsembler2/
Any comment/feedback is warmly welcome.