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
http://en.wikipedia.org/wiki/Sequence_assembly
short reads assembler
http://cab.spbu.ru/software/spades/
microbial community assembly (metagenomics)
https://github.com/voutcn/megahit
Scaffolding pre-assembled contigs using SSPACE
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information.
http://www.baseclear.com/bioinformatics-tools
Fast assembler for small genomes
https://github.com/dzerbino/velvet
Designed for assembling large plant and animal genomes
http://soap.genomics.org.cn/soapdenovo.html
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