Update parameters (#378)

* Update parameters

Co-authored-by: Lauren Coombe <lauren.e.coombe@gmail.com>

Author: Vladimir Nikolić

README.md

@@ -474,14 +474,14 @@ Parameters of the driver script, `abyss-pe`
  * `kc`: minimum k-mer count threshold for Bloom filter assembly [`2`]
  * `K`: the length of a single k-mer in a k-mer pair (bp)
  * `l`: minimum alignment length of a read (bp) [`40`]
- * `m`: minimum overlap of two unitigs (bp) [`0` (interpreted as `k - 1`)]
+ * `m`: minimum overlap of two unitigs (bp) [`0` (interpreted as `k - 1`) if `mp` is provided or if `k<=50`, otherwise `50`]
  * `n`: minimum number of pairs required for building contigs [`10`]
- * `N`: minimum number of pairs required for building scaffolds [`n`]
+ * `N`: minimum number of pairs required for building scaffolds [`15-20`]
  * `np`: number of MPI processes [`1`]
  * `p`: minimum sequence identity of a bubble [`0.9`]
  * `q`: minimum base quality [`3`]
  * `s`: minimum unitig size required for building contigs (bp) [`1000`]
- * `S`: minimum contig size required for building scaffolds (bp) [`1000-10000`]
+ * `S`: minimum contig size required for building scaffolds (bp) [`100-5000`]
  * `t`: maximum length of blunt contigs to trim [`k`]
  * `v`: use `v=-v` for verbose logging, `v=-vv` for extra verbose
  * `x`: spaced seed (Bloom filter assembly only)

bin/abyss-pe

@@ -153,6 +153,9 @@ endif
 endif
 
 pe?=$(lib)
+ifdef mp
+  mp_provided=1
+endif
 mp?=$(pe)
 
 # Strip spaces from the file paths
@@ -233,7 +236,13 @@ abyssopt += $(dbopt) $(SS) --coverage-hist=coverage.hist -s $*-bubbles.fa
 endif
 
 # AdjList parameters
-m?=0
+ifdef mp_provided
+  m?=0
+else ifeq ($(shell test $(k) -le 50; echo $$?),0)
+  m?=0
+else
+  m?=50
+endif
 alopt += $v $(dbopt) $(SS) -k$k -m$m
 ifndef B
 ifdef K
@@ -337,8 +346,8 @@ mcopt += $v $(dbopt) -k$k
 
 # Scaffold parameters
 L?=$l
-S?=1000-10000
-N?=$n
+S?=100-5000
+N?=15-20
 SCAFFOLD_DE_S?=$(shell echo $S | sed 's/-.*//')
 SCAFFOLD_DE_N?=$N
 SCAFFOLD_DE_OPTIONS?=$(DISTANCEEST_OPTIONS)