Effaln

version 0.1 (20220915)
version 0.2 (20231022)
version 0.3 (20231205)

What is it?

Effaln is an efficient Burrows-Wheeler-based mapper for longer Next-generation sequencing reads.

How to use it?

Effaln consists of two components, index building and read mapping. You should first build the FM-index with the reference genome, and then perform the mapping process.

Step I. Install

Download (or clone) the source code form https://github.com/guolilu3/Effaln
Compile the source code. (Note that you need to compile semiWFA first)
```
cd ./semiWFA   
make

cd ../
make
```

Step II. Build FM-index

Run the shell command:
```
./effaln-index <refName> <idxName>
```
where refName is the reference genome, idxName is the index file name.

Step III. Mapping

Run the shell command:
```
./effaln -x <idxName> -U <rdsName> -S <samName>
```
where idxName is the index file name, rdsName is the sequencing reads file name, and samName is the mapping result file name.

Feedback

Please report bugs to Email: guolilu@stu.xidian.edu.cn or jgxygll@163.com if any questions or suggestions.
Your feedback and test results are welcome.

License

Effaln is available under the MIT license.

Name		Name	Last commit message	Last commit date
Latest commit History 4 Commits
hasheb		hasheb
semiWFA		semiWFA
third_party		third_party
BaseClass.h		BaseClass.h
BitMap.cpp		BitMap.cpp
BitMap.h		BitMap.h
InArray.cpp		InArray.cpp
InArray.h		InArray.h
README.md		README.md
aligner_bt.cpp		aligner_bt.cpp
aligner_bt.h		aligner_bt.h
aligner_cache.cpp		aligner_cache.cpp
aligner_cache.h		aligner_cache.h
aligner_driver.cpp		aligner_driver.cpp
aligner_driver.h		aligner_driver.h
aligner_metrics.h		aligner_metrics.h
aligner_report.h		aligner_report.h
aligner_result.cpp		aligner_result.cpp
aligner_result.h		aligner_result.h
aligner_seed.cpp		aligner_seed.cpp
aligner_seed.h		aligner_seed.h
aligner_seed2.cpp		aligner_seed2.cpp
aligner_seed2.h		aligner_seed2.h
aligner_seed_policy.cpp		aligner_seed_policy.cpp
aligner_seed_policy.h		aligner_seed_policy.h
aligner_sw.cpp		aligner_sw.cpp
aligner_sw.h		aligner_sw.h
aligner_sw_common.h		aligner_sw_common.h
aligner_sw_driver.cpp		aligner_sw_driver.cpp
aligner_sw_nuc.h		aligner_sw_nuc.h
aligner_swsse.cpp		aligner_swsse.cpp
aligner_swsse.h		aligner_swsse.h
aln_build.cpp		aln_build.cpp
aln_idx.cpp		aln_idx.cpp
aln_idx.h		aln_idx.h
aln_io.cpp		aln_io.cpp
aln_search.cpp		aln_search.cpp
aln_search.h		aln_search.h
aln_sink.cpp		aln_sink.cpp
aln_sink.h		aln_sink.h
aln_util.cpp		aln_util.cpp
alphabet.cpp		alphabet.cpp
alphabet.h		alphabet.h
assert_helpers.h		assert_helpers.h
binary_sa_search.h		binary_sa_search.h
bitpack.h		bitpack.h
blockwise_sa.h		blockwise_sa.h
btypes.h		btypes.h
build_main.cpp		build_main.cpp
ccnt_lut.cpp		ccnt_lut.cpp
const.h		const.h
diff_sample.cpp		diff_sample.cpp
diff_sample.h		diff_sample.h
dolen.sh		dolen.sh
dp_framer.cpp		dp_framer.cpp
dp_framer.h		dp_framer.h
ds.cpp		ds.cpp
ds.h		ds.h
edit.cpp		edit.cpp
edit.h		edit.h
effaln-index		effaln-index
embedding.cpp		embedding.cpp
embedding.h		embedding.h
endian_swap.h		endian_swap.h
fast_mutex.h		fast_mutex.h
filebuf.h		filebuf.h
formats.h		formats.h
group_walk.cpp		group_walk.cpp
group_walk.h		group_walk.h
hasheb5		hasheb5
header.h		header.h
ival_list.cpp		ival_list.cpp
ival_list.h		ival_list.h
ksw2.h		ksw2.h
ksw2_extz2_sse.c		ksw2_extz2_sse.c
limit.cpp		limit.cpp
limit.h		limit.h
loadkit.cpp		loadkit.cpp
loadkit.h		loadkit.h
ls.cpp		ls.cpp
ls.h		ls.h
main.cpp		main.cpp
makefile		makefile
mask.cpp		mask.cpp
mask.h		mask.h
mem_ids.h		mem_ids.h
mm.h		mm.h
multikey_qsort.cpp		multikey_qsort.cpp
multikey_qsort.h		multikey_qsort.h
opts.h		opts.h
outq.cpp		outq.cpp
outq.h		outq.h
pat.cpp		pat.cpp
pat.h		pat.h
pe.cpp		pe.cpp
pe.h		pe.h
presets.cpp		presets.cpp
presets.h		presets.h
processor_support.h		processor_support.h
qual.cpp		qual.cpp

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