diff --git a/a50.cabal b/a50.cabal
--- a/a50.cabal
+++ b/a50.cabal
@@ -1,5 +1,5 @@
 Name:           a50
-Version:        0.2
+Version:        0.4
 License:        GPL
 
 Author:         Ketil Malde
@@ -21,15 +21,16 @@
 		.
                 The Darcs repository is at <http://malde.org/~ketil/biohaskell/a50>.
 
--- HomePage:	http://blog.malde.org/area50
-Build-Depends:  base>=3 && <5, bio > 0.4, process, containers, cmdargs >= 0.5, directory
+HomePage:	http://blog.malde.org/index.php/a50-a-graphical-comparison-of-genome-assemblies
 Build-Type:     Simple
 Cabal-Version:	>= 1.2.3
 Tested-with:    GHC==6.12.1
-
 Data-files:     README
-Executable:     a50
-Main-Is:        A50.hs
-Other-Modules:	Gnuplot, Options, Blat
-Hs-Source-Dirs: src
-Ghc-Options:    -Wall
+
+Executable a50
+    Main-Is:        A50.hs
+    Other-Modules:  Gnuplot, Options, Blat, Sort
+    Hs-Source-Dirs: src
+    Ghc-Options:    -Wall
+    Build-Depends:  base>=3 && <5, bio > 0.4, process, containers, cmdargs >= 0.5, directory
+
diff --git a/src/A50.hs b/src/A50.hs
--- a/src/A50.hs
+++ b/src/A50.hs
@@ -1,13 +1,12 @@
 module Main where
 
-import Bio.Sequence
-import Data.List (intersperse, foldl')
-
-import qualified Data.IntMap as M
+import Data.List (intersperse)
 
 import Gnuplot
 import Blat
-import Options
+import Sort    (sizes, sort, SizeTable)
+import Options (Opt(..), getArgs)
+import Control.Monad (when)
 
 main :: IO ()
 main = do 
@@ -15,16 +14,32 @@
   ss <- mapM sizes $ inputs opts
   case estref opts of 
     "" -> do
+      when (format opts /= "plot") $ n50 (map read $ expect opts) $ zip (inputs opts) ss
       mkplot opts $ map (each 10) $ map ((scanl1 (+)) . sort) ss
     est -> do  
       ps <- mapM (\asm -> fmap gen_result $ runBlat (tmpdir opts) asm est) (inputs opts)
       mkplot opts $ map (each 10) $ map (scanl1 (+)) $ zipWith interleave (map sort ss) ps
   -- putStr $ zipLists fs (map ((scanl1 (+)) . sort) ss)
 
-each :: Int -> [a] -> [a]
-each _ [] = []
-each n (x:xs) = x : each n (drop (n-1) xs)
+n50 :: [Int] -> [(FilePath,SizeTable)] -> IO ()
+n50 [e] iss = do
+  let genOut (f,st) = putStrLn (f ++ "\t"++go [e`div`4,e`div`2,3*e`div`4] (scanl1 (+) $ sort st))
+      go (e0:es) (z1:z2:zs) = 
+        if z2 > e0 then show (z2-z1)++"\t"++go es (z1:z2:zs)
+        else go (e0:es) (z2:zs)
+      go [] (z1:z2:zs) = z1 `seq` go [] (z2:zs)
+      go es [z1] = concatMap (const "-\t") es ++ show z1++" total size"
+      go _ []  = error "shouldn't happen"
+  putStrLn ("Assembly \tn25\tn50\tn75\t\testimated size="++show e)
+  mapM_ genOut iss
+n50 _ _ = return ()
 
+each :: Int -> [a] -> [(Int,a)]
+each k = go 0
+  where
+    go _ [] = []
+    go i (x:xs) = (i,x) : go (i+k) (drop (k-1) xs)
+
 zipLists :: [String] -> [[Int]] -> String
 zipLists fs ss = unlines ((concat $ map ("#\t"++) fs) : go (map (++repeat 0) ([1..]:ss)))
   where go :: [[Int]] -> [String]
@@ -33,28 +48,16 @@
                 in if all (==0) $ tail hs then []
                    else (concat $ intersperse "\t" $ map myshow hs) : go ts
 
-myshow :: Integral i => i -> String
+myshow :: (Integral i, Show i) => i -> String
 myshow 0 = ""
 myshow n = show n
 
-mkplot :: Opt -> [[Int]] -> IO ()
-mkplot o ns = gnuplot [conf,outp,labels,tics] (zip (inputs o) ns) es
+mkplot :: Opt -> [[(Int,Int)]] -> IO ()
+mkplot o ns = let my_out = if format o == "plot" then gnudat else gnuplot
+              in my_out [conf,outp,labels,tics] (zip (inputs o) ns) es
   where labels = "set ylabel 'cumulative size'; set xlabel 'contig number'"
-        tics  = "set format y '%.0s%c'; set format x '%.0f0'"
-        conf = if null $ format o then "" else "set terminal "++format o
+        tics  = "set format y '%.1s%c'; set format x '%.0f'"
+        conf = if (null $ format o) || format o == "plot" then "" else "set terminal "++format o
         outp = if null $ outfile o then "" else "set out '"++outfile o++"'"
         es   = map read $ expect o
                   
-sizes :: FilePath -> IO [Int]
-sizes f = map (fromIntegral . seqlength) `fmap` readFasta f
-
-sort :: [Int] -> [Int]
-sort = concatMap (\(x,c) -> replicate c (fromIntegral $ negate x)) . M.toAscList . freqs
-
--- equivalent to  'M.fromList . map (\x->(fromIntegral $ negate x,1))', 
--- except for not blowing the stack
-freqs :: [Int] -> M.IntMap Int
-freqs = foldl' ins M.empty . map fromIntegral . map negate
-  where ins m x = case M.lookup x m of 
-          Just v -> v `seq` M.insert x (v+1) m
-          Nothing -> M.insert x 1 m
diff --git a/src/Blat.hs b/src/Blat.hs
--- a/src/Blat.hs
+++ b/src/Blat.hs
@@ -19,11 +19,12 @@
 runBlat tmpdir asm ests = do
   let pslfile = tmpdir++"/"++basename asm++"_vs_"++basename ests++".psl"
       basename = reverse . takeWhile (/='/') . reverse
+      quote str = "\""++str++"\""
   dfe <- doesFileExist pslfile
   when (not dfe) $ do
     fe <- findExecutable "blat"
     when (fe == Nothing) $ error "Couldn't find the 'blat' executable - aborting"
-    blat <- runCommand $ unwords [blat_cmd,asm,ests,pslfile]
+    blat <- runCommand $ unwords (blat_cmd : map quote [asm,ests,pslfile])
     e <- waitForProcess blat
     case e of ExitSuccess -> return ()
               _ -> error $ show e
@@ -33,7 +34,7 @@
 gen_result :: [PSL] -> [(Int,Int)]
 gen_result = coverage . order . pslbest
 
-interleave :: Integral i => [i] -> [(i,i)] -> [i]
+interleave :: (Integral i, Show i) => [i] -> [(i,i)] -> [i]
 interleave sz [] = map (const 0) sz
 interleave (sz:szs) covs@((s1,c1):cs) 
   | sz > s1   = 0 : interleave szs covs
diff --git a/src/Gnuplot.hs b/src/Gnuplot.hs
--- a/src/Gnuplot.hs
+++ b/src/Gnuplot.hs
@@ -9,7 +9,7 @@
 import System.Directory (findExecutable)
 import Control.Concurrent (forkIO)
 
-gnuplot :: Num i => [String] -> [(String,[i])] -> [Int] -> IO ()
+gnuplot :: (Show i, Num i) => [String] -> [(String,[(Int,i)])] -> [Double] -> IO ()
 gnuplot preamble cols hlines = do
   fe <- findExecutable "gnuplot"
   when (fe == Nothing) $ error "Couldn't find the 'gnuplot' executable - aborting"
@@ -17,24 +17,29 @@
   _ <- forkIO (hGetContents o >>= hPutStr stdout)
   -- ugly hack to limit error output
   _ <- forkIO $ do 
-    let go ~(l1:l2:ls) =do putStrLn l1
-                           if ('^' `elem` l1) 
-                             then do 
-                               putStrLn l2
-                             else go (l2:ls)
+    let go ~(l1:l2:ls) = do putStrLn l1
+                            if ('^' `elem` l1)
+                              then do
+                                putStrLn l2
+                              else go (l2:ls)
     go =<< fmap lines (hGetContents e)
-
-  
-  hPutStr i $ unlines $ preamble
-  hPutStrLn i (mkplots cols ++ concatMap ((',':) . show) hlines)
-  mapM_ (\col -> do {hPutStr i . unlines . map show . snd $ col; hPutStrLn i "e"}) cols
-
+  genplot i preamble cols hlines
   hClose i
-
   x <- waitForProcess p
   case x of ExitSuccess ->  return ()
             ExitFailure j -> hPutStrLn stderr (errmsg++show j) >> return ()
     where errmsg = "'gnuplot' failed with exit code "
+
+gnudat :: (Show i, Num i) => [String] -> [(String,[(Int,i)])] -> [Double] -> IO ()
+gnudat = genplot stdout
+
+-- | Write gnuplot instructions to a handle (todo: make pure)
+genplot :: (Show i, Num i) => Handle -> [String] -> [(String,[(Int,i)])] -> [Double] -> IO ()
+genplot i preamble cols hlines = do
+  hPutStr i $ unlines $ preamble
+  let show' (x,y) = show x ++ "\t" ++ show y
+  hPutStrLn i (mkplots cols ++ concatMap ((',':) . show) hlines)
+  mapM_ (\col -> do {hPutStr i . unlines . map show' . snd $ col; hPutStrLn i "e"}) cols
 
 -- | generate the plot command
 mkplots :: [(String,[a])] -> String
diff --git a/src/Options.hs b/src/Options.hs
--- a/src/Options.hs
+++ b/src/Options.hs
@@ -5,7 +5,7 @@
 import System.Console.CmdArgs
 import Control.Monad (when)
 import System.Directory (getTemporaryDirectory)
-import Foreign (unsafePerformIO)
+import System.IO.Unsafe (unsafePerformIO)
 
 tmpdefault :: FilePath
 tmpdefault = unsafePerformIO getTemporaryDirectory
@@ -38,7 +38,8 @@
 setOutputFormat o 
   | null (format o) && null (outfile o) = o
   | null (format o)                     = o { format = determineFormat $ outfile o }
-  | null (outfile o)                    = error "Please specify an output file (-o) when you specify format."
+  | format o /= "plot" && null (outfile o) = error "Please specify an output file (-o) when you specify format."
+  | format o == "plot" && not (null $ outfile o) = error "'plot' format isn't supported with '-o',\nand only writes to standard output."
   | otherwise       = o
     where 
       determineFormat fp =
diff --git a/src/Sort.hs b/src/Sort.hs
new file mode 100644
--- /dev/null
+++ b/src/Sort.hs
@@ -0,0 +1,21 @@
+module Sort where
+
+import qualified Data.IntMap as M
+import Bio.Sequence
+import Data.List (foldl')
+
+type SizeTable = M.IntMap Int
+
+sizes :: FilePath -> IO SizeTable
+sizes f = (freqs . map (fromIntegral . seqlength)) `fmap` readFasta f
+
+sort :: SizeTable -> [Int]
+sort = concatMap (\(x,c) -> replicate c (fromIntegral $ negate x)) . M.toAscList
+
+-- equivalent to  'M.fromList . map (\x->(fromIntegral $ negate x,1))', 
+-- except for not blowing the stack
+freqs :: [Int] -> SizeTable
+freqs = foldl' ins M.empty . map fromIntegral . map negate
+  where ins m x = case M.lookup x m of 
+          Just v -> v `seq` M.insert x (v+1) m
+          Nothing -> M.insert x 1 m