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malonge
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RagTag
Tools for fast and flexible genome assembly scaffolding and improvement
MIT License
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integration with juicer
#191
Overcraft90
opened
2 days ago
0
Scaffold option -r error
#190
arif-tanmoy
closed
2 weeks ago
0
question of Hi-C to resolve conflicts
#189
njliangdong
opened
1 month ago
0
`updategff` produces wrong output if parts of the scaffolds are used in the AGP file
#188
taprs
opened
1 month ago
0
RagTag error: "OSError: error when opening file"
#187
ylzou867
opened
1 month ago
0
Adjust default gap size
#186
mrvollger
closed
2 months ago
1
ragtag.patch.fasta lacks unplaced contigs?
#185
adadiehl
closed
1 month ago
1
Missing ragtag.correct.reads.s.bam file
#184
faye-romero
opened
3 months ago
1
Scaffold and correct
#183
aabaricalla
opened
3 months ago
1
ragtag_scaffold.py: error: unrecognized arguments
#182
athenasyarifa
opened
3 months ago
0
output file not found
#181
Anysdn
opened
4 months ago
0
The scaffold command was submitted and the assembled result was not available
#180
LZY19940813
opened
4 months ago
1
Using RagTag to close the gaps in a chromosome or reference genome using long-read data
#179
gforg34
opened
6 months ago
0
Speed RagTag up a few orders of magnitude on fragmented assemblies with caching
#178
twrightsman
opened
8 months ago
1
Ragtag Merge IndexError for -f AGP file
#177
nickgladman
opened
8 months ago
0
ERROR: encountered an invalid zero or negative numeric AGP field.
#176
wshuai294
closed
8 months ago
1
patch output genome is identical to input target genome
#175
wackerk
opened
9 months ago
1
Error when running RagTag patch command
#174
nvuhunganh
closed
9 months ago
1
pysam error
#173
mabh5
opened
9 months ago
0
Scaffold longer than reference genome due to NNNNs
#172
vappiah
opened
11 months ago
3
Can't use multiple threads via -t
#171
ChungLamYu
opened
11 months ago
3
Scaffolding inserts gaps that aren't covered by HiFi or ONT reads and aren't in reference
#170
nickgladman
closed
10 months ago
7
the result of ragtag.merge.fasta shows no improvement.
#169
zhangkaihui1
opened
1 year ago
0
`ragtag scaffold` without concatenation
#168
taprs
opened
1 year ago
0
From delta file to agp and to fasta file of scaffolded assembly?
#167
hrpelg
opened
1 year ago
0
updategff issues
#166
El-Castor
opened
1 year ago
0
Stop without error message on "Reading whole genome alignments"
#165
Wzuoqi
opened
1 year ago
0
Unable to fill gap with ragtag scaffold and patch
#164
yipukangda
opened
1 year ago
0
correct use by the species.
#163
danielpinilla1
opened
1 year ago
1
RagTAg correct: "no attribute 'get_reference_length'"
#162
pna059
closed
1 year ago
1
Running RagTag on bacterial short-read assemblies
#161
ne1al
opened
1 year ago
0
Large >270Mb contigs vs >14Gb reference
#160
Ural-Yunusbaev
opened
1 year ago
0
Question about installation
#159
zhousun21
opened
1 year ago
1
A question about "correct" step in RagTag, I need help!
#158
link-xhx
closed
5 months ago
3
Scaffold inserting strings of 100 N's?
#157
cizydorczyk
closed
1 year ago
3
Ragtag.py merge RuntimeError: only complete components can be added to the graph error
#156
benyoung93
opened
1 year ago
6
RagTag patch bug
#155
r-poloni
opened
1 year ago
4
Scaffold doesn't run
#154
aebaci
closed
1 year ago
1
Cases where missassembly correction and patching aren't needed
#153
sjfleck
closed
1 year ago
1
Patch error: "Tuple Index out of Range"
#152
schmigle
opened
1 year ago
1
How to pass minimap2 parameters?
#151
evo-eco-gen
closed
1 year ago
1
repeat masking
#150
evo-eco-gen
closed
1 year ago
1
RagTag name coming up
#149
rmormando
opened
1 year ago
0
Some contigs are not scaffolded
#148
rknx
opened
1 year ago
0
RagTag Reference
#147
WeixuanPlant
closed
1 year ago
1
Error message when running ragtag_scaffold.py
#146
Surbhigrewal
opened
1 year ago
0
Scaffolding error: 'RuntimeError: There are no useful alignments. Check output alignment files.`
#145
bahiyahazli
closed
1 year ago
3
about paf2delta
#144
1085268616
opened
1 year ago
1
Can RagTag use for improve assembled contigs from macrogenomes or macrotrasncriptome
#143
NailouZhang
opened
1 year ago
0
Split assembly at BED coordinates
#142
Neato-Nick
opened
1 year ago
1
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