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molikd
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otb
Only The Best (Genome Assembly Tools)
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fixes in polishing branch fcs_adaptor processes
#65
dluecke
closed
4 months ago
0
Bug fixes to enable yahs scaffolding
#64
dluecke
closed
5 months ago
0
yahs not finding inter-contig links due to missorted aln.bam file
#63
dluecke
closed
5 months ago
1
Pipeline not starting scaffolding steps due to missing --scaffold flag
#62
dluecke
closed
5 months ago
1
HiC forward/reverse read files swapped in run.nf HiFiASM call
#61
dluecke
closed
7 months ago
1
Possible issue with $BUSCO check in template.slurm files
#60
dluecke
opened
8 months ago
1
Singularity library cache environmental variables not propagating to scripts
#59
dluecke
opened
8 months ago
0
Multiple BAM inputs cause bad link to data
#58
dluecke
opened
8 months ago
0
Updated gitignore, slurm template
#57
SharuPaul
closed
1 year ago
0
juicer pre needs to be run again
#56
molikd
closed
1 year ago
0
FCS-adaptor process add
#55
molikd
closed
1 year ago
1
otb.sh doesn't handle wildcards handover to nextflow
#54
molikd
closed
2 years ago
0
procedures for major tool changes and versioning for otb genomes
#53
molikd
closed
2 years ago
1
generate the hic files
#52
molikd
closed
2 years ago
7
ragtag patch step is hella slow.
#51
molikd
closed
2 years ago
4
env_check needs to check NXF_SINGULARITY_LIBRARYDIR, added to slurm scritps and tutorials
#50
molikd
closed
2 years ago
2
process K_mer_counting filt_fastq_ch needs to be flattened so that all input hifi reads are k-mer counted.
#49
molikd
closed
2 years ago
1
contributions wiki page and README
#48
molikd
closed
2 years ago
2
ragtag on haplotypes for scaffolding should be optional.
#47
molikd
closed
2 years ago
2
gfa2fasta error in phasing mode
#46
molikd
closed
2 years ago
0
otb.sh now checks files
#45
molikd
closed
2 years ago
0
otb.sh needs to be updated for hic/mat/pat reads
#44
molikd
closed
2 years ago
1
Dev
#43
molikd
closed
2 years ago
0
add -l to the params
#42
molikd
closed
2 years ago
0
Bring in gfastats --seq-report?
#41
Astahlke
closed
2 years ago
5
Is ragtag a good default component?
#40
Astahlke
closed
2 years ago
2
Find a better small test dataset
#39
Astahlke
closed
2 years ago
8
otb.run.lite.slum file
#38
molikd
closed
2 years ago
0
Bring in components of nf-core?
#37
Astahlke
closed
2 years ago
3
Ag100pest recommendations or standard workflow in wiki
#36
molikd
closed
1 year ago
8
--lite doesn't process in HiFiASM
#35
molikd
closed
2 years ago
2
Build out bwa mem short read aligner container
#34
Astahlke
closed
2 years ago
5
minimap_for_yahs needs hic reads, not hifi
#33
Astahlke
closed
2 years ago
4
trio mode needs parental reads, not hic
#32
Astahlke
closed
2 years ago
3
Fixes for #28 and #29
#31
Astahlke
closed
2 years ago
0
rewrite check fastq process?
#30
molikd
closed
2 years ago
2
update hifiadapterfilt
#29
Astahlke
closed
2 years ago
2
genome scope should be run on filtered Hifi data
#28
molikd
closed
2 years ago
2
rebuild slum_usda config
#27
molikd
closed
2 years ago
2
otb.sh and run.nf conversion to use multiple HiFi reads files instead of just two
#26
molikd
closed
2 years ago
1
make sure you can run without hic
#25
molikd
closed
2 years ago
5
Check "homozygous", and "heterozygous" options for HiFiASM, possibly not reading the HiFi reads?
#24
molikd
closed
2 years ago
4
The hifi data input format only the bam format ？
#23
zhangwenda0518
closed
2 years ago
2
memory limits with hifiasm
#22
molikd
closed
2 years ago
4
Create a Two Lined Genome assembly with OTB
#21
molikd
closed
1 year ago
10
add zenodo to otb
#20
molikd
closed
2 years ago
1
update reports and results on wiki page
#19
molikd
closed
2 years ago
1
yahs flag/getopts build out
#18
molikd
closed
2 years ago
1
shhquis flag/getopts build out
#17
molikd
closed
2 years ago
1
ragtag make contigs equal in length to polished genome steps flag/getopts build out
#16
molikd
closed
2 years ago
0
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