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BWA-FastAlign
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update readme

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zzh 2025-08-31 18:12:47 +08:00
parent 9afd9ed39c
commit 807c32066a
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5
Makefile
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@ -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

8
README.md
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@ -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