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broadinstitute
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pilon
Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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BUG pilon renames headers in fasta, adds "|pilon"
#173
Luky1228
closed
1 month ago
1
What does "Large collapsed region" mean in standard output?
#172
ryanskiba
opened
1 month ago
0
Pilon died mid-run
#171
drdna
opened
2 months ago
0
Polish a large genome with Pilon
#170
enriquepola1996
opened
3 months ago
2
Pilon Killed with no other error message
#169
dorie8
opened
4 months ago
1
Java out of memory
#168
JWang52md
opened
5 months ago
0
Memory problem
#167
Wanjie-Feng
opened
7 months ago
0
Pilon is running but no .changes file in output
#166
NicMAlexandre
closed
2 months ago
0
pilon freezes and doesnt respond
#165
Vasudha-pai
opened
9 months ago
0
an error?I use pilon to polish my ONT—data assembly genome. Then I got the line: Exception in thread "main" java.lang.IllegalStateException: Inappropriate call if not paired read.so what can I do next.my bam file has some error?
#164
sugarsaman
opened
9 months ago
0
pilon error:Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
#163
smoothyly
opened
10 months ago
0
Exception in thread "main" java.lang.NoSuchMethodError: java.nio.ByteBuffer.position(I)Ljava/nio/ByteBuffer;
#162
karthickbrlab
closed
12 months ago
0
unable to access jarfile pilon-1.24.jar
#161
tbazilegith
opened
1 year ago
2
HashMap table size
#160
rivabros2
opened
1 year ago
0
Java heap space error while running pilon
#159
saras224
opened
1 year ago
0
Asking for indexed bam file
#158
saras224
opened
1 year ago
1
pilon error: Exception in thread "main" java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary: contig_1
#157
saras224
opened
1 year ago
1
Error with very short contig
#156
bartns
opened
1 year ago
0
Segmenting genome for quicker result
#155
tamsinlh
opened
1 year ago
0
How to resume
#154
methylome
opened
1 year ago
0
no bam file
#153
rmormando
opened
1 year ago
1
Question: Are redundant bases inside overlapping ends of paired reads counted once or twice towards consensus?
#152
JohnUrban
opened
2 years ago
0
fasta headers not appended but overwritten
#151
hkaspersen
opened
2 years ago
0
Index -1 out of bounds for length X
#150
anitajnorman
opened
2 years ago
1
Memory usage relation to file size?
#149
snail123815
opened
2 years ago
1
Make polishing stats machine-readable
#148
kim-fehl
opened
2 years ago
0
--threads argument no longer supported
#147
cpavloud
closed
1 year ago
1
Correct spelling mistakes
#146
EdwardBetts
opened
2 years ago
0
VCF format issue
#145
jodyphelan
opened
2 years ago
0
"main" java.lang.IllegalArgumentException: requirement failed
#144
bioramg
opened
2 years ago
2
Pilon on haplotype polish: how did pilon deal with haplotype genome assembly?
#143
cjchen5
opened
2 years ago
0
Fix vcf header def for DP
#142
jodyphelan
opened
2 years ago
0
VCF header issue
#141
jodyphelan
opened
2 years ago
0
Problem with executing Pilon
#140
Hai1983
opened
2 years ago
2
Pilon on transcriptome assembly from tetraploid species
#139
ConcettaDe4
opened
2 years ago
0
How to run pilon
#138
leggylas
closed
2 years ago
2
Issues running pilon
#137
myco-bradshaw
opened
2 years ago
0
Discordant Pilon Results for Equivalent Files
#136
cwarden45
opened
3 years ago
0
Annotate allelic depth?
#135
pgcudahy
opened
3 years ago
1
Ways to speed up pilon
#134
kattweigh
opened
3 years ago
1
trying to polish nanopore with illumina don't understand the error
#133
Ayse1006
opened
3 years ago
2
Absurdly long run time and GCLocker
#132
NTNguyen13
opened
3 years ago
1
Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.io.FileNotFoundException: align_filer.bam
#131
zhuanghemu
opened
3 years ago
1
HI
#130
zhuanghemu
opened
3 years ago
0
Pilon appearing to make no corrections or confimations of bases
#129
Rob-murphys
opened
3 years ago
1
java.lang.OutOfMemoryError
#128
kjestradag
opened
3 years ago
3
Can you go into more detail about the --threads option? What does "experimental" mean?
#127
lfaller-zymergen
opened
3 years ago
2
Does pilon write to temp files?
#126
lfaller-zymergen
opened
3 years ago
1
Expected memory usage
#125
nhartwic
closed
3 years ago
4
Exception in thread "main" java.nio.BufferUnderflowException
#124
francescodc87
opened
4 years ago
2
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