Easily get coverage from velvet assemblies

gistfile1.md

• assemble data and output an AMOS file (-amos_file yes)

• download and build http://sourceforge.net/projects/amos/

• convert the afg file output by velvet to a bnk file

   ~/src/amos-3.0.0/src/Bank/bank-transact -m my.afg -b my.bnk -c
  

• get short-version, depth-of-coverage output

   ~/src/amos-3.0.0/src/Validation/analyze-read-depth my.bnk -d
  

• if you need coverage across specific contigs, you can get a "map" of node number (velvet) to IID (amos) by outputting data as follows:

   ~/src/amos-3.0.0/src/Utils/cvgStat -b my.bnk > my.cvg
  

• then parse that file to match iid to node number. after parsing pass the IID data (here named *.iid) to analyze-read-depth for the contigs in which you are interested

   ~/src/amos-3.0.0/src/Validation/analyze-read-depth my.bnk -d -I my.iid