Fast spliced aligner with low memory requirements
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doc
example
hisat.xcodeproj
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.gitattributes
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MANUAL
MANUAL.markdown
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README.md
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aligner_bt.cpp
aligner_bt.h
aligner_cache.cpp
aligner_cache.h
aligner_driver.cpp
aligner_driver.h
aligner_metrics.h
aligner_report.h
aligner_result.cpp
aligner_result.h
aligner_seed.cpp
aligner_seed.h
aligner_seed2.cpp
aligner_seed2.h
aligner_seed_policy.cpp
aligner_seed_policy.h
aligner_sw.cpp
aligner_sw.h
aligner_sw_common.h
aligner_sw_driver.cpp
aligner_sw_driver.h
aligner_sw_nuc.h
aligner_swsse.cpp
aligner_swsse.h
aligner_swsse_ee_i16.cpp
aligner_swsse_ee_u8.cpp
aligner_swsse_loc_i16.cpp
aligner_swsse_loc_u8.cpp
aln_sink.cpp
aln_sink.h
alphabet.cpp
alphabet.h
assert_helpers.h
banded.cpp
banded.h
binary_sa_search.h
bitpack.h
blockwise_sa.h
bowtie_build_main.cpp
bowtie_main.cpp
bp_aligner.h
bt2_build.cpp
bt2_idx.cpp
bt2_idx.h
bt2_inspect.cpp
bt2_io.h
bt2_search.cpp
bt2_util.h
btypes.h
ccnt_lut.cpp
classifier_li.h
diff_sample.cpp
diff_sample.h
dp_framer.cpp
dp_framer.h
ds.cpp
ds.h
edit.cpp
edit.h
endian_swap.h
extract_splice_sites.py
fast_mutex.h
filebuf.h
formats.h
group_walk.cpp
group_walk.h
hi_aligner.h
hier_idx.h
hier_idx_common.h
hisat
hisat-build
hisat-inspect
hisat.cpp
hisat_bp.cpp
hisat_build.cpp
hisat_build_main.cpp
hisat_inspect.cpp
hisat_main.cpp
ival_list.cpp
ival_list.h
limit.cpp
limit.h
ls.cpp
ls.h
make
mask.cpp
mask.h
mem_ids.h
mm.h
multikey_qsort.cpp
multikey_qsort.h
opts.h
outq.cpp
outq.h
pat.cpp
pat.h
pe.cpp
pe.h
presets.cpp
presets.h
processor_support.h
qual.cpp
qual.h
random_source.cpp
random_source.h
random_util.cpp
random_util.h
read.h
read_qseq.cpp
ref_coord.cpp
ref_coord.h
ref_read.cpp
ref_read.h
reference.cpp
reference.h
sam.cpp
sam.h
scoring.cpp
scoring.h
search_globals.h
sequence_io.h
shmem.cpp
shmem.h
simple_func.cpp
simple_func.h
splice_site.cpp
splice_site.h
splice_site_mem.h
splice_site_new.cpp
spliced_aligner.h
sse_util.cpp
sse_util.h
sstring.cpp
sstring.h
str_util.h
threading.h
timer.h
tinythread.cpp
tinythread.h
tokenize.h
unique.cpp
unique.h
util.h
word_io.h
zbox.h

README.md

hisat

HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover the whole genome (each index represents a genomic region of ~64,000 bp and ~48,000 indexes are needed to cover the human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons. The memory footprint of HISAT is relatively low (~4.3GB for the human genome). I have developed HISAT based on the Bowtie2 implementation to handle most of the operations on the FM index.