Omega2 Pipeline

Omega2  metagenome assembly pipeline requires 3 steps:
Read merging using STORM

Download: https://bitbucket.org/yaoornl/align_test/overview

STORM is a tool for merging paired-end reads with variable insert sizes (i.e. for both overlapping and non-overlapping pairs)​. It calculates the read overlaps and calls the consensus. The advantage is that it can merge the non-overlapping reads with a third read connecting them. But it’s slower and needs more memory compare to k-mer method like BBMerge.

Error Correction using HERO

Download: https://github.com/guo-xuan/Hero

HERO is a multi-threaded and multiprocess distributed sequencing read correction tool. It calculates the alignments between possible overlapped reads and calls the consensus. The advantage of HERO is that it can correct sequencing errors according to more reliable alignment than K-mers and also can estimate the sequencing coverage.
Metagenome Assembly using DISCO

Download: https://github.com/abiswas-odu/Disco

DISCO is a multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler. Disco was developed as a scalable assembler to assemble large metagenomes from billions of Illumina sequencing reads of complex microbial communities.

Overlap-graph de novo Assembler for Metagenomics