From 807c32066a97b7dd007a48d17cc172dc0ffeb284 Mon Sep 17 00:00:00 2001 From: zzh Date: Sun, 31 Aug 2025 18:12:47 +0800 Subject: [PATCH] update readme --- Makefile | 5 +++-- README.md | 8 ++++---- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/Makefile b/Makefile index 6b2a454..07b79b5 100644 --- a/Makefile +++ b/Makefile @@ -17,11 +17,12 @@ AOBJS= bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ bwtsw2_chain.o fastmap.o bwtsw2_pair.o profiling.o \ fmt_idx.o ksw_extend2_avx2.o ksw_extend2_avx2_u8.o \ debug.o -PROG= fastbwa +PROG= fastalign INCLUDES= LIBS= -lm -lz -lpthread -ldl SUBDIRS= . -JE_MALLOC=/home/zzh/work/jemalloc/lib/libjemalloc.a +#JE_MALLOC=/home/zzh/work/jemalloc/lib/libjemalloc.a +JE_MALLOC= ifeq ($(shell uname -s),Linux) LIBS += -lrt diff --git a/README.md b/README.md index ba268a5..e2dbe88 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,11 @@ -# FastBWA +# FastAlign Fast alignment tool based on bwa-mem # 1. Compile the source code make -j 8 # 2. Build the FMT-Index -./fastbwa index reference.fasta +./fastalign index reference.fasta -# 3. Run sequence alignment with fastBWA -./fastbwa mem -t 64 -2 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:fastbwa reference.fasta r1.fq.gz r2.fq.gz +# 3. Run sequence alignment with FastAlign +./fastalign mem -t 64 -2 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:fastbwa reference.fasta r1.fq.gz r2.fq.gz