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Issues: malonge/RagTag

Troubleshooting inaccurate scaffolds
#48 by malonge was closed Mar 1, 2021
Closed
Providing a precomputed PAF file for scaffolding
#86 by mrvollger was closed Nov 2, 2021
Closed 2
Why not use Nucmer 4?
#93 by Yutang-ETH was closed Dec 31, 2021
Closed 8
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69 Open 110 Closed
69 Open 110 Closed
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Issues list

Missing ragtag.correct.reads.s.bam file
#184 opened Jul 11, 2024 by faye-romero
Scaffold and correct
#183 opened Jul 6, 2024 by aabaricalla
1
ragtag_scaffold.py: error: unrecognized arguments
#182 opened Jun 24, 2024 by athenasyarifa
output file not found
#181 opened Jun 20, 2024 by Anysdn
The scaffold command was submitted and the assembled result was not available
#180 opened Jun 18, 2024 by LZY19940813
1
Using RagTag to close the gaps in a chromosome or reference genome using long-read data
#179 opened Apr 8, 2024 by gforg34
Ragtag Merge IndexError for -f AGP file
#177 opened Feb 7, 2024 by nickgladman
patch output genome is identical to input target genome
#175 opened Jan 11, 2024 by wackerk
pysam error
#173 opened Dec 29, 2023 by mabh5
Scaffold longer than reference genome due to NNNNs
#172 opened Nov 20, 2023 by vappiah
3
Can't use multiple threads via -t
#171 opened Nov 17, 2023 by ChungLamYu
3
the result of ragtag.merge.fasta shows no improvement.
#169 opened Sep 6, 2023 by zhangkaihui1
ragtag scaffold without concatenation
#168 opened Sep 4, 2023 by taprs
From delta file to agp and to fasta file of scaffolded assembly?
#167 opened Aug 27, 2023 by hrpelg
updategff issues
#166 opened Jul 31, 2023 by El-Castor
Stop without error message on "Reading whole genome alignments"
#165 opened Jun 6, 2023 by Wzuoqi
Unable to fill gap with ragtag scaffold and patch
#164 opened May 31, 2023 by yipukangda
correct use by the species.
#163 opened May 29, 2023 by danielpinilla1
1
Running RagTag on bacterial short-read assemblies
#161 opened Apr 24, 2023 by ne1al
Large >270Mb contigs vs >14Gb reference
#160 opened Apr 13, 2023 by Ural-Yunusbaev
Question about installation
#159 opened Apr 12, 2023 by zhousun21
1
Ragtag.py merge RuntimeError: only complete components can be added to the graph error
#156 opened Mar 10, 2023 by benyoung93
6
RagTag patch bug
#155 opened Mar 2, 2023 by r-poloni
3
Patch error: "Tuple Index out of Range"
#152 opened Feb 6, 2023 by schmigle
1
RagTag name coming up
#149 opened Jan 17, 2023 by rmormando
ProTip! no:milestone will show everything without a milestone.