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Added recommendation for PacBio reads

This commit is contained in:
Heng Li 2011-01-22 13:20:11 -05:00
parent dac5395126
commit 7fd8948689
2 changed files with 6 additions and 2 deletions
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6
bwtsw2_main.c
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@ -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) {

2
main.c
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@ -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()