mapsembler
bioinformatics targeted assembly software
Install
- All systems
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curl cmd.cat/mapsembler.sh
- Debian
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apt-get install mapsembler2 - Ubuntu
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apt-get install mapsembler2 - Kali Linux
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apt-get install mapsembler2 - Windows (WSL2)
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sudo apt-get updatesudo apt-get install mapsembler2 - Raspbian
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apt-get install mapsembler2 - Dockerfile
- dockerfile.run/mapsembler
mapsembler2
bioinformatics targeted assembly software
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