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cgroza
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GraffiTE
GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
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Output read-names supporting the individual inserts (and deletions) per sample
#48
natenstuff
closed
4 days ago
2
Question about './work directory storage issue'
#47
xxYaaoo
opened
1 week ago
1
Process `tsd_search` terminated even with enough memory
#46
amnghn
closed
1 week ago
6
Update minimap2 to allow lr:hq mode
#45
annabel-NZ
closed
4 weeks ago
4
Speedup repmask_vcf.sh
#44
Han-Cao
closed
1 month ago
2
Bug in calculating TE match lengths
#43
Han-Cao
closed
1 month ago
6
Could GraffiTE identify de novo TE insertions using short reads?
#42
LeoHongboWANG
closed
1 month ago
1
My TE-associated DEL is much lesster than TE-associated INS
#41
cuiyangkai
closed
1 month ago
3
ERROR ~ Error executing process > 'map_asm (27)'
#40
rpianezza
closed
1 month ago
7
repmask_vcf.sh creating empty indels.fa file (longreads run ending at tsd_prep)
#39
tiagonardi
closed
3 months ago
3
Long read mapping: Broken pipe
#38
TobyBaril
closed
2 months ago
5
FATAL: Extraction failed (cache disk quote issue)
#37
TobyBaril
closed
3 months ago
2
Suggestion: Return TSD=None for easy parsing
#36
acontrerasg
opened
3 months ago
1
ERROR : Failed to create user namespace: user namespace disabled
#35
qizhengyang2017
closed
1 week ago
13
Singularity issue
#34
qizhengyang2017
closed
4 months ago
8
ERROR ~ Error executing process > 'graph_align_reads (41)'
#33
yykaya
opened
4 months ago
7
New variations after genotyping.
#32
tongyin121
closed
4 months ago
4
GraffiTE stops at the tsd_prep step when bypassing SV discovery
#31
SarahBailey1998
opened
6 months ago
6
Replace `pangenome.vcf` with a `presence-absence.vcf` as main output, but keep it to build the graph genomes
#30
clemgoub
opened
6 months ago
0
does GraffiTE work with 10x linked reads?
#29
Lin-Yuying
closed
5 months ago
1
TE library construction and Input file quality control
#28
abcyulongwang
closed
6 months ago
2
Fixes from bugs I encountered
#27
mikecuoco
closed
6 months ago
2
GraffiTE exiting at minimap due to "Unknown option: --no-home"
#26
jamesdgalbraith
closed
3 months ago
10
Provide variants coordinates for all input genomes, not only reference (as in the VCF)
#25
RRebo
opened
6 months ago
1
3_TSD_search output folder missing
#24
Wicker-Lab
opened
7 months ago
3
Question about setting own tmp dir
#23
xxYaaoo
closed
4 months ago
13
prepTSD filters
#22
cgroza
closed
8 months ago
0
How to interpret the results of the TIPs genotyping
#21
dtx282000
closed
9 months ago
5
Inquiry about Integrating Minigraph-cactus into the Pipeline for Enhanced SV Analysis
#20
porkfan
closed
3 months ago
6
Error for PanGenie-index
#19
dtx282000
closed
9 months ago
3
Winnowmap
#18
cgroza
closed
10 months ago
0
Tmpdir
#17
cgroza
closed
10 months ago
0
[E::parse_cigar] CIGAR length too long at position 1 (274808464H)
#16
davidaray
closed
6 months ago
14
genotyping with assemblies only
#15
davidaray
closed
1 year ago
1
short reads question
#14
Spieler2999
closed
1 year ago
1
singularity issue
#13
Spieler2999
closed
1 year ago
6
GraffiTE ended at repeatmask vcf: Error executing process > 'repeatmask_VCF (1)' Caused by: Process `repeatmask_VCF (1)` terminated with an error exit status (255)
#12
shenmeguimlf
closed
1 year ago
10
Typo L481 of main.nf
#11
YannBourgeois
closed
1 year ago
1
max divergence options
#10
acontrerasg
closed
1 year ago
5
GraffiTE ends prematurely at "tsd_prep" with no output. [FIXED: check chromosome names]
#9
clemgoub
closed
1 year ago
1
Possible issue related to $TMPDIR
#8
dewuem
closed
1 year ago
15
Graphaligner
#7
cgroza
closed
2 years ago
0
Current singularity image bug: `biomartr` missing
#6
clemgoub
closed
2 years ago
0
Giraffe
#5
cgroza
closed
2 years ago
0
Error "Argument of `file` function cannot be null"
#4
Tcvalenzuela
closed
2 years ago
4
The need to gzipped files
#3
Tcvalenzuela
closed
2 years ago
1
Update giraffe with latest defintion file.
#2
cgroza
closed
2 years ago
0
singularity guide
#1
Tcvalenzuela
closed
2 years ago
2