MariaNattestad Assemblytics issues

MariaNattestad / Assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

http://assemblytics.com

MIT License

134 stars 28 forks source link

issues

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Web browser not working

#62 winkle38 opened 2 months ago
0
The case where the sequence strand of SV is a reverse strand

#61 jwli-code closed 3 months ago
6
delta files problem

#60 Gon1976 closed 3 months ago
3
Fix log file permissions to run pipeline in background

#59 MariaNattestad closed 5 months ago
0
Track examples in git repo

#58 MariaNattestad closed 5 months ago
0
Difference between the 'within_alignment' and the 'between_alignment' methods

#57 LeoVincenzi opened 7 months ago
3
Error Running Assemblytics_within_alignment.py

#56 jiaanqiang closed 5 months ago
2
What are ref gap size , query gap size and ref_start and ref_stop for tandem expansion and tandem contractions?

#55 mariaelf97 closed 5 months ago
1
Repeat Contractions and Expansions are the most frequent call in a bacterial genome

#54 derekcg closed 1 year ago
1
Stuck on "Checking progress"

#53 bmansfeld closed 5 months ago
1
Why some "insertion"s reported by assemblytics have length of zero?

#52 mariaelf97 closed 1 year ago
4
add judgement about strand;fix query coord

#51 wjwei-handsome opened 1 year ago
0
Coordinates in the negative strand are not correct

#50 wjwei-handsome closed 5 months ago
1
No file uploaded

#49 weilu1998 closed 5 months ago
15
I upload a delta file, I get the error message "No file uploaded."

#48 ITGMT closed 5 months ago
1
Confirmation parameters of nucmer

#47 qingyun-mei closed 5 months ago
0
Update Assemblytics_dotplot.R

#46 thdurand4 opened 2 years ago
0
Tandem contraction

#45 rillaxy opened 2 years ago
0
Issue with coordinates of variants

#44 MartuGio closed 5 months ago
1
Server not available

#43 anleopa closed 5 months ago
2
Bed file coordinate system

#42 agolicz opened 2 years ago
2
Variants with the same coordinates

#41 kyleLesack closed 3 years ago
2
R and Python versions

#40 shabirmoosa closed 5 months ago
1
Assemblytics for bacterial genome

#39 rthapa1 closed 5 months ago
1
Can I detect the Inversion?

#38 shehongbing closed 3 years ago
1
Failed file upload - Is the Assemblytics server down?

#37 Neato-Nick closed 5 months ago
12
What does diagonal red lines/dots mean in interactive plot?

#36 MehmetGoktay closed 4 years ago
1
Output bed file has no chromosomes in the first column

#35 lxxiaoxiaLi closed 4 years ago
3
Identification of tandem duplications

#34 MehmetGoktay closed 4 years ago
1
Unauthenticated File upload Vulnerability

#33 ghost closed 4 years ago
1
Some lines without reference information in the bed file

#32 ShuaishuaiTai closed 4 years ago
0
'Potentially' the same variant called as a deletion and an tandem expansion

#31 AyushSaxena closed 4 years ago
1
Understanding output bed file

#30 ViriatoII closed 4 years ago
5
Assembly statistics mismatch

#29 cssulliv closed 4 years ago
3
Which tool was used to identify repeats and tandem repeats in the genome?

#28 AyushSaxena closed 4 years ago
3
Maximum variant size

#27 MehmetGoktay closed 4 years ago
4
Python 3 fixes

#26 MariaNattestad closed 4 years ago
0
`TypeError: list indices must be integers or slices, not float` with uncompressed delta file

#25 0xaf1f closed 4 years ago
2
UnicodeDecodeError when using compressed delta file

#24 0xaf1f closed 4 years ago
4
UnicodeDecodeError when using compressed delta file

#23 0xaf1f closed 4 years ago
1
Consolidate web version, update to python3

#22 MariaNattestad closed 4 years ago
0
differences between the web and CLI version of the engine

#21 0xaf1f closed 4 years ago
3
assemblytics uses python 2

#20 0xaf1f closed 4 years ago
2
script for modifying a genome with known SVs

#19 liufy11 closed 5 years ago
1
Assemblytics within-alignments SVs

#18 GaoLei-bio closed 5 years ago
6
Any tools to convert Assemblytics bed output to vcf format?

#17 JunpengShi closed 5 years ago
7
Regarding the parameters in Assemblytics.

#16 koushik1989 closed 5 years ago
1
Does it have to be a delta file

#15 peflanag closed 5 years ago
3
Output variant sequences

#14 CWYuan08 closed 5 years ago
1
input assembly stats from assemblytics

#13 chunlinxiao closed 5 years ago
1