hifiasm

xxay/hifiasm

Fork 0

mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-28 21:28:11 +08:00

T

Haoyu Cheng dc67fc6d2b test readme

2019-12-26 14:31:00 -05:00

.vscode

final DP-based assembly

2019-11-13 20:18:11 -05:00

.gitignore

added gitignore

2019-12-26 09:41:15 -05:00

Assembly.cpp

fixed clang warnings

2019-12-26 09:40:35 -05:00

Assembly.h

clean code

2019-12-26 02:26:24 -05:00

CommandLines.cpp

clean code

2019-12-26 02:26:24 -05:00

CommandLines.h

clean code

2019-12-26 02:26:24 -05:00

Correct.cpp

fixed clang warnings

2019-12-26 09:40:35 -05:00

Correct.h

clean code

2019-12-26 02:26:24 -05:00

Hash_Table.cpp

clean code

2019-12-26 02:26:24 -05:00

Hash_Table.h

clean code

2019-12-26 02:26:24 -05:00

kdq.h

final DP-based assembly

2019-11-13 20:18:11 -05:00

ketopt.h

Using klib

2019-05-10 16:14:01 -04:00

khash.h

clean code

2019-12-26 02:26:24 -05:00

kmer.cpp

final DP-based assembly

2019-11-13 20:18:11 -05:00

kmer.h

clean code

2019-12-26 02:26:24 -05:00

kseq.h

added klib_unused to suppress kseq warnings

2019-11-22 14:47:54 -05:00

ksort.h

final DP-based assembly

2019-11-13 20:18:11 -05:00

kvec.h

final DP-based assembly

2019-11-13 20:18:11 -05:00

Levenshtein_distance.cpp

clean code

2019-12-26 02:26:24 -05:00

Levenshtein_distance.h

fixed clang warnings

2019-12-26 09:40:35 -05:00

LICENSE

Initial commit

2019-05-09 15:34:58 -04:00

main.cpp

clean code

2019-12-26 02:26:24 -05:00

Makefile

clean code

2019-12-26 02:26:24 -05:00

Output.cpp

clean code

2019-12-26 02:26:24 -05:00

Output.h

full error correction

2019-07-14 21:13:50 -04:00

Overlaps.cpp

fix TODO

2019-12-26 12:42:50 -05:00

Overlaps.h

clean code

2019-12-26 02:26:24 -05:00

POA.cpp

clean code

2019-12-26 02:26:24 -05:00

POA.h

clean code

2019-12-26 02:26:24 -05:00

Process_Read.cpp

fixed clang warnings

2019-12-26 09:40:35 -05:00

Process_Read.h

clean code

2019-12-26 02:26:24 -05:00

README.md

test readme

2019-12-26 14:31:00 -05:00

README.md

Getting Started

# Install hifiasm and miniasm (requiring g++ and zlib)
git clone https://github.com/chhylp123/hifiasm.git
cd hifiasm && make
# Assembly (corrected reads are at NA12878.asm.fa, assembly graph is at NA12878.asm.fa.gfa)
./hifiasm -w -l -q NA12878.fq.gz -o NA12878.asm.fa -k 40 -t 32 -r 2 -a 4 -z 0