diff --git a/ChangeLog b/ChangeLog index 03574fe92..91857714a 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,21 @@ +2018-11-09 Ben Vandervalk + + * Release version 2.1.4 + * Major improvements to Bloom filter assembly contiguity and + correctness. Bloom filter assemblies now have equivalent scaffold + contiguity and better correctness than MPI assemblies of the same + data, while still requiring less than 1/10th of the memory. On + human, Bloom filter assembly times are still a few hours longer + than MPI assemblies (e.g. 17 hours vs. 13 hours, using 48 + threads). + + abyss-pe: + * Change default value of `m` from 50 => 0, which has the effect + of disallowing sequence overlaps < k-1 bp. QUAST tests on E. coli / + C. elegans / H. sapiens showed that both contiguity and + correctness were improved by allowing only overlaps of k-1 bp + between sequence ends. + 2018-11-05 Ben Vandervalk * Release version 2.1.3 diff --git a/Misc/samtobreak.hs b/Misc/samtobreak.hs index e7893f5ba..e5a14ca03 100644 --- a/Misc/samtobreak.hs +++ b/Misc/samtobreak.hs @@ -279,7 +279,7 @@ parseArgs = do where help = putStr (usageInfo usage options) >> exitSuccess tryHelp = "Try 'abyss-samtobreak --help' for more information." - version = "abyss-samtobreak (ABySS) 2.1.3\n" + version = "abyss-samtobreak (ABySS) 2.1.4\n" usage = "Usage: samtobreak [OPTION]... [FILE]...\n\ \Calculate contig and scaffold contiguity and correctness metrics.\n" diff --git a/bin/abyss-pe b/bin/abyss-pe index f3126edce..663f425be 100755 --- a/bin/abyss-pe +++ b/bin/abyss-pe @@ -395,7 +395,7 @@ help: @echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users@bcgsc.ca.' version: - @echo "abyss-pe (ABySS) 2.1.3" + @echo "abyss-pe (ABySS) 2.1.4" @echo "Written by Shaun Jackman and Anthony Raymond." @echo @echo "Copyright 2012 Canada's Michael Smith Genome Science Centre" diff --git a/configure.ac b/configure.ac index 127bcc197..b9bdc74f9 100644 --- a/configure.ac +++ b/configure.ac @@ -1,5 +1,5 @@ AC_PREREQ(2.62) -AC_INIT(ABySS, 2.1.3, abyss-users@bcgsc.ca, abyss, +AC_INIT(ABySS, 2.1.4, abyss-users@bcgsc.ca, abyss, http://www.bcgsc.ca/platform/bioinfo/software/abyss) m4_include(m4/m4_ax_pthread.m4) AM_INIT_AUTOMAKE(1.9.6 foreign subdir-objects) @@ -263,7 +263,7 @@ elif test x"$enable_werror" = x"yes"; then AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra -Werror') else # default - AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra -Werror') + AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra') fi # Build abyss-paired-dbg and abyss-paired-dbg-mpi diff --git a/doc/ABYSS.1 b/doc/ABYSS.1 index 7cf97705a..65a5ed46c 100644 --- a/doc/ABYSS.1 +++ b/doc/ABYSS.1 @@ -1,4 +1,4 @@ -.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.1.3" "User Commands" +.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.1.4" "User Commands" .SH NAME ABYSS \- assemble short reads into contigs .SH SYNOPSIS diff --git a/doc/abyss-pe.1 b/doc/abyss-pe.1 index 15ecd1d6e..07fe73159 100644 --- a/doc/abyss-pe.1 +++ b/doc/abyss-pe.1 @@ -1,4 +1,4 @@ -.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.1.3" "User Commands" +.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.1.4" "User Commands" .SH NAME abyss-pe - assemble reads into contigs .SH SYNOPSIS diff --git a/doc/abyss-tofastq.1 b/doc/abyss-tofastq.1 index 3ae4637b5..68c5f8a32 100644 --- a/doc/abyss-tofastq.1 +++ b/doc/abyss-tofastq.1 @@ -1,4 +1,4 @@ -.TH abyss-tofastq "1" "2015-May" "ABySS 2.1.3" "User Commands" +.TH abyss-tofastq "1" "2015-May" "ABySS 2.1.4" "User Commands" .SH NAME abyss-tofastq \- convert various file formats to FASTQ format .br