Genome assembling

Aligning and merging short fragments of sequenced DNA in order to reconstruct the original genome.

    • reference-mapping approach

      • mapping reads to reference genomes

    • de novo assembly approach

      • assembling reads without help of a similar reference sequence

read more

http://en.wikipedia.org/wiki/Sequence_assembly

→ N50 statistics

Tools

SPAdes

short reads assembler

http://cab.spbu.ru/software/spades/

microbial community assembly (metagenomics)

https://github.com/voutcn/megahit

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

SSPACE

Scaffolding pre-assembled contigs using SSPACE

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information.

http://www.baseclear.com/bioinformatics-tools

Velvet

Fast assembler for small genomes

https://github.com/dzerbino/velvet

SOAPdenovo

Designed for assembling large plant and animal genomes

http://soap.genomics.org.cn/soapdenovo.html


read more

https://en.wikipedia.org/wiki/Sequence_assembly

Comparison and algorithmic background of assemblers

http://www.illumina.com/Documents/products/technotes/technote_denovo_assembly_ecoli.pdf