##Ebola Virus Makona Genome Assembly and Analysis

EBOV Makona genomes were assembled from high-throughput sequencing data using an updated bioinformatics pipeline based on our previously described methods \citep{Gire_2014, Matranga_2014}. Of the collected samples, 150 KGH and 82 CDC samples were used to accumulate sufficient EBOV genome sequencing coverage for high quality de novo genome assembly. Further description of the pipeline can be found in the Extended Experimental Procedures.

Our Linux-based software pipeline is publicly available at https://github.com/broadinstitute/viral-ngs \citep{zenodo_viral_ngs}. This pipeline includes command-line tools for each of the above steps and optional Snakemake workflows \citep{Koster_2012} to automate them either sequentially or in parallel.

The assembly pipeline is also available via the DNAnexus cloud platform. RNA paired-end reads from either HiSeq or MiSeq instruments (Illumina) can be securely uploaded in FASTQ or BAM format and processed through the pipeline using graphical and command-line interfaces. Instructions for the cloud analysis pipeline are available at https://github.com/dnanexus/viral-ngs/wiki