From 7fd894868928db7f61fcff693963d7ee2f84f0ed Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 22 Jan 2011 13:20:11 -0500 Subject: [PATCH] Added recommendation for PacBio reads --- bwtsw2_main.c | 6 +++++- main.c | 2 +- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/bwtsw2_main.c b/bwtsw2_main.c index 0f1c660..afbad2e 100644 --- a/bwtsw2_main.c +++ b/bwtsw2_main.c @@ -59,7 +59,11 @@ int bwa_bwtsw2(int argc, char *argv[]) fprintf(stderr, " -N INT # seeds to trigger reverse alignment [%d]\n", opt->t_seeds); fprintf(stderr, " -c FLOAT coefficient of length-threshold adjustment [%.1f]\n", opt->coef); fprintf(stderr, " -H in SAM output, use hard clipping rather than soft\n"); - fprintf(stderr, " -f FILE file to output results to instead of stdout\n"); + fprintf(stderr, " -f FILE file to output results to instead of stdout\n\n"); + fprintf(stderr, "Note: For long Illumina, 454 and Sanger reads, assembly contigs, fosmids and\n"); + fprintf(stderr, " BACs, the default setting usually works well. For the current PacBio\n"); + fprintf(stderr, " reads (end of 2010), '-b5 -q2 -r1 -z10' is recommended. One may also\n"); + fprintf(stderr, " increase '-z' for better sensitivity.\n"); fprintf(stderr, "\n"); if (0) { diff --git a/main.c b/main.c index af5cc37..a87d1a1 100644 --- a/main.c +++ b/main.c @@ -3,7 +3,7 @@ #include "main.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.5.9rc1-r12" +#define PACKAGE_VERSION "0.5.9rc1-r15" #endif static int usage()