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Mapsembler

Mapsembler


Mapsembler2 is a targeted assembly software. It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent 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 gene (input as starter) has an homolog in a set of reads
· 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
· Remove contaminants or symbiont reads from a read set


Access mode(s):

Command line on saruman.versailles.inra.fr

Update: 03 Feb 2014
Creation date: 30 Jan 2014