cmonjeau/mapsembler2 repository overview

###Mapsembler2 description:

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, …

###Mapsembler2 website: https://colibread.inria.fr/software/mapsembler2/⁠

###Mapsembler2 Docker Github: https://github.com/cmonjeau/docker-mapsembler2⁠

###Run Mapsembler2 with docker: docker run -it --rm cmonjeau/mapsembler2