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4. scaffolding  5. verification of scaffolds/contigs   The first step simply removes poor quality sequences, as well as adaptor sequences left over from sequencing. Some assemblers follow this with error correction where reads are compared to each other to eliminate sequencing errors. Next is contig assembly where overlapping reads are assembled into long continuous streches stretches  of sequences. Scaffolding refers to the alignment and orientation of these contigs relative to each other (where possible). The last step is verification where reads are mapping back to the contigs/scaffolds to eliminate misassemblies. There is a plethora of programs that can perform some, or most of these steps. These programs include commercial and open-source options, some are very user friendly and some are extremely difficult to use/install. Common assemblers for bacterial genomes include SPAdes \cite{Bankevich_2012}, MIRA \cite{Chevreux_2004}, SGA \cite{Simpson_2010}, Velvet \cite{Zerbino_2008} CLC (CLC Bio), and A5 \cite{Tritt_2012}. Good sources for overviews of genome assemblers and the assembly process include the GAGE project \cite{Salzberg_2012}, the GAGE-B project \cite{Magoc_2013}, and the Assemblathon Project \cite{Earl_2011}.