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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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74 Open 113 Closed
74 Open 113 Closed
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Issues list

The possibility of starting from HiFi ccs reads
#192 opened Nov 5, 2024 by OceanLyu
integration with juicer
#191 opened Oct 17, 2024 by Overcraft90
question of Hi-C to resolve conflicts
#189 opened Sep 18, 2024 by njliangdong
updategff produces wrong output if parts of the scaffolds are used in the AGP file
#188 opened Sep 13, 2024 by taprs
RagTag error: "OSError: error when opening file"
#187 opened Sep 4, 2024 by ylzou867
Missing ragtag.correct.reads.s.bam file
#184 opened Jul 11, 2024 by faye-romero
1
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
1
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
ProTip! Exclude everything labeled bug with -label:bug.