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DaehwanKimLab
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hisat2
Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
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HISAT2 Repeat API. Support MacOS
#189
parkchanhee
closed
5 years ago
0
Add c++ library
#188
parkchanhee
closed
5 years ago
0
Repeat API for Python, Java
#187
parkchanhee
closed
5 years ago
0
Add cmath header to suppress warnings about abs()
#186
parkchanhee
closed
5 years ago
0
Seed
#185
parkchanhee
closed
5 years ago
0
v2.0.5: Referencing large indexes via environment variable `HISAT2_INDEXES` appears broken
#184
ebzheng
closed
5 years ago
1
Hisat2
#183
ndp13
closed
5 years ago
1
Reference genome masking
#182
fbrundu
closed
5 years ago
1
align is running even if index is broken
#181
juancresc
opened
6 years ago
1
Read has more quality values than read characters
#180
juancresc
closed
5 years ago
1
Wrong calculation for NM tag
#179
sergiigladchuk
opened
6 years ago
0
Recommended options for bacterial RNA-seq
#178
apredeus
opened
6 years ago
0
Output file is still generated when there is a error
#177
hsiaoyi0504
opened
6 years ago
0
Python scripts should be Python3 compatible
#176
pvanheus
closed
5 years ago
1
Definition of MapQ missing
#175
bernt-matthias
opened
6 years ago
0
--interleaved Option
#174
ATpoint
opened
6 years ago
6
How to detect expression of a rare variant?
#173
biocyberman
opened
6 years ago
0
rna-strandness default
#172
bernt-matthias
closed
6 years ago
0
HISAT2 Multi/Unique Mapping
#171
StevenWingett
opened
6 years ago
0
A sra file can not get complete SAM.
#170
chenzhenxia119
closed
6 years ago
0
HISAT-genotype using custom variants
#169
igordot
opened
6 years ago
6
add make install target
#168
wookietreiber
opened
6 years ago
0
Fixup # of index files in the manual/docs.
#167
nh13
opened
6 years ago
0
Hisat2 binary not executable on Mac OS High Sierra 10.13.4
#166
ttamho
opened
6 years ago
0
uninitialised value $l in scalar chomp
#165
KatyBrown
opened
6 years ago
0
Bug using --novel-splicesite-outfile : wrong left side of an intron reported
#164
Juke34
closed
5 years ago
2
no documentation of --avoid-pseudogene option
#163
bzip2
opened
6 years ago
0
High RAM usage during indexing and function of exon file
#162
suryasaha
opened
6 years ago
2
Cleanup child processes, when the hisat2(wrapper) terminated
#161
parkchanhee
closed
6 years ago
1
Replace "bowtie" with "HISAT2"
#160
hlfernandez
closed
6 years ago
1
--tmo problem with hisat2 version 2.1.0 but not 2.0.4
#159
sgivan
opened
6 years ago
0
Hisat2 processes won't fully die - Linux server
#158
megan-kc
opened
6 years ago
1
Replaced "bowtie" with "hisat2"
#157
molecules
closed
6 years ago
1
Removed commandline options version 2.0.3 vs >=2.0.5
#156
mmterpstra
opened
6 years ago
0
Retaining multi-mapping reads
#155
willhooper
opened
6 years ago
1
number of mismatch
#154
YuanwenGuo
closed
6 years ago
2
--new-summary option contains the SAM scores
#153
MatteoSchiavinato
opened
6 years ago
0
Does hisat2 support colorspace reads?
#152
apredeus
closed
6 years ago
1
Multi-mapped reads
#151
manuelsmendoza
closed
6 years ago
0
Allow Hisat 2 to detect compression & filetype automatically
#150
ambrosejcarr
opened
6 years ago
0
hisat2 hangs on bad options when stdout is piped
#149
knightjimr
closed
6 years ago
2
Tutorial for HISAT2 (not bowtie2)
#148
molecules
closed
6 years ago
1
hisat2-build segfault during indexing
#147
BioComSoftware
opened
6 years ago
0
--no-unal option not shown in the help, but found in the script
#146
MatteoSchiavinato
opened
6 years ago
0
Trouble using HISAT2 - "internal HISAT2 exception (#1)" and "(ERR): hisat2-align exited with value 1"
#145
manuelsmendoza
closed
6 years ago
4
hisat2-align died with signal 6 (ABRT)
#144
gianfilippo
opened
6 years ago
0
Special Alignment
#143
sagnikbanerjee15
opened
6 years ago
0
`flag > 0` for `const char * flag`
#142
BenLangmead
closed
6 years ago
1
Compressed / Uncompressed fastq input without -U option
#141
joachimwolff
closed
5 years ago
0
Too hard to make a known splice site infile
#140
ewallace
opened
7 years ago
0
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