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结合fmt-index，pattern-based sw优化，低内存占用，高性能的序列比对程序，结果与bwa-mem一致
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zzh 9afd9ed39c modify readme 2025-01-14 14:36:02 +08:00
.vscode Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwakit Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
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COPYING Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
ChangeLog Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
LICENSE Initial commit 2025-01-14 14:28:47 +08:00
Makefile Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
NEWS.md Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
QSufSort.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
QSufSort.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
README-alt.md Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
README.md Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bamlite.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bamlite.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bntseq.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bntseq.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwa.1 Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwa.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwa.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwamem.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwamem.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwamem_extra.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwamem_pair.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwape.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwase.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwase.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwaseqio.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwashm.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwt.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwt.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwt_gen.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwt_lite.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwt_lite.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwtaln.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwtaln.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwtgap.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwtgap.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwtindex.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwtsw2.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwtsw2_aux.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwtsw2_chain.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwtsw2_core.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwtsw2_main.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
bwtsw2_pair.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
code_of_conduct.md Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
debug.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
debug.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
example.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
fastmap.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
fmt_idx.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
fmt_idx.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
h.txt Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
is.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
kbtree.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
khash.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
kopen.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
kseq.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
ksort.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
kstring.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
kstring.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
ksw.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
ksw.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
ksw_align_avx2.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
ksw_extend2_avx2.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
ksw_extend2_avx2_u8.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
kthread.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
kvec.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
main.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
malloc_wrap.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
malloc_wrap.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
maxk.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
neon_sse.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
pemerge.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
profiling.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
profiling.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
qualfa2fq.pl Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
rle.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
rle.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
rope.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
rope.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
run.sh Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
scalar_sse.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
utils.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
utils.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
xa2multi.pl Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
yarn.c Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00
yarn.h Fast NGS sequence alignment tool based on bwa-mem. 2025-01-14 14:34:09 +08:00

README.md

FastBWA

Fast alignment tool based on bwa-mem

1. Compile the source code

make -j 8

2. Build the FMT-Index

./fastbwa 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