mapsembler2

About mapsembler2

From Debian's package description

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

From Debian's description of the mapsembler2 package, under that package's license.