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BWA-FastAlign
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update readme

This commit is contained in:
zzh 2025-08-31 18:12:47 +08:00
parent 9afd9ed39c
commit 807c32066a
2 changed files with 7 additions and 6 deletions
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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 \ bwtsw2_chain.o fastmap.o bwtsw2_pair.o profiling.o \
fmt_idx.o ksw_extend2_avx2.o ksw_extend2_avx2_u8.o \ fmt_idx.o ksw_extend2_avx2.o ksw_extend2_avx2_u8.o \
debug.o debug.o
PROG= fastbwa PROG= fastalign
INCLUDES= INCLUDES=
LIBS= -lm -lz -lpthread -ldl LIBS= -lm -lz -lpthread -ldl
SUBDIRS= . SUBDIRS= .
JE_MALLOC=/home/zzh/work/jemalloc/lib/libjemalloc.a #JE_MALLOC=/home/zzh/work/jemalloc/lib/libjemalloc.a
JE_MALLOC=
ifeq ($(shell uname -s),Linux) ifeq ($(shell uname -s),Linux)
LIBS += -lrt LIBS += -lrt

8
README.md
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@ -1,11 +1,11 @@
# FastBWA # FastAlign
Fast alignment tool based on bwa-mem Fast alignment tool based on bwa-mem
# 1. Compile the source code # 1. Compile the source code
make -j 8 make -j 8
# 2. Build the FMT-Index # 2. Build the FMT-Index
./fastbwa index reference.fasta ./fastalign index reference.fasta
# 3. Run sequence alignment with fastBWA # 3. Run sequence alignment with FastAlign
./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 ./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