started assembly tuto

Author: HadrienG

assembly.md

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+# Whole-genome de-novo Assembly
+
+In this practical we will perform the assembly of M. genitalium, a bacterium published in 1995 by Fraser et al in Science.
+
+## Getting the data
+
+Go to ENA, and search for the run ERR486840.
+
+Download the 2 fastq files associated with the run.
+
+## Quality control?
+
+How many reads are in the fastq file? What is the read length?
+Does the data need trimming or other filtering? If so, do it.
+
+Find the genome size of M. genitalium in the Fraser paper abstract.
+Based on the expected genome size, the read length and the number of reads – what average coverage do you expect to get from this fastq read files?
+
+## De-novo assembly
+
+We will be using the SPAdes assembler to assemble our bacterium.
+
+This will produce a series of outputs. The scaffolds will be in fasta format.
+
+How well does the assembly total consensus size and coverage correspond to your earlier estimation?
+What is the N50 of the assembly? What does this mean?
+How many contigs in total did the assembly produce?
+How many contigs longer than 500bp? What is the N50 of those contigs only?
+
+Perform more assemblies with the following options:
+
+Raw reads (no trimming, but with adapters removed), let spades do the qc.
+
+## Comparing assemblies
+
+quast
+
+### Comparing to the reference?
+
+Get the reference fasta here
+
+## Fixing misassemblies?