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pdimens
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harpy
Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.
https://pdimens.github.io/harpy
GNU General Public License v3.0
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[simulate linkedreads] consider swapping dwgsim for ngsngs
#137
pdimens
opened
4 days ago
1
purge empty log files
#136
pdimens
closed
1 week ago
0
log changes and fixes
#135
pdimens
closed
1 week ago
1
add --threads to [resume]
#134
pdimens
closed
1 week ago
0
biallelic contig finder has false positives
#133
pdimens
closed
1 week ago
0
compress snakemake logs
#132
pdimens
closed
1 week ago
0
harpy sv naibr IndexError: list index out of range
#131
azwadriqbal
closed
2 weeks ago
4
tidy up impute
#130
pdimens
closed
3 weeks ago
0
add and style progress spinners
#129
pdimens
closed
3 weeks ago
0
fix reports
#128
pdimens
closed
3 weeks ago
0
report improvements
#127
pdimens
closed
3 weeks ago
0
advanced progressbar
#126
pdimens
closed
1 month ago
0
add a progress bar
#125
pdimens
closed
1 month ago
0
[align] add option to keep unmapped reads
#124
pdimens
closed
1 month ago
1
[snp] ploidy conflicts with extra params
#123
pdimens
closed
1 month ago
1
metagenome assembly
#122
pdimens
opened
1 month ago
1
provide copy of log file into output directory
#121
pdimens
closed
1 month ago
1
[SV] sample grouping not using phased bams
#120
pdimens
closed
1 month ago
1
Bam merge fix
#119
pdimens
closed
1 month ago
0
blog post on SV grouping
#118
pdimens
closed
1 month ago
0
[SV] manually deconvolve MI for merge
#117
pdimens
closed
1 month ago
0
add file validation for --genome fasta file
#116
pdimens
closed
1 month ago
1
custom filenames for DT csv exports
#115
pdimens
closed
1 month ago
0
[reports] give all tables with CSV output custom filename
#114
pdimens
closed
1 month ago
0
Mergevariants
#113
pdimens
closed
1 month ago
0
[sv naibr] consolidate bedpe output
#112
pdimens
closed
1 month ago
0
convert circlize + plotly to BioCircos
#111
pdimens
closed
1 month ago
0
Svplots
#110
pdimens
closed
2 months ago
0
[SV] interactive variant plots as single plots with dropdowns
#109
pdimens
closed
2 months ago
1
rm ggplot and ggridges code
#108
pdimens
closed
2 months ago
0
[phase] ridgeplot replacement
#107
pdimens
closed
2 months ago
0
[phase] retain sites with less than or more than 2 alleles
#106
pdimens
closed
1 month ago
0
[phase] --vcf-samples not working correctly
#105
pdimens
closed
2 months ago
1
[phase] --genome error
#104
pdimens
closed
2 months ago
1
Deconvolute
#103
pdimens
closed
2 months ago
0
Deconvolute
#102
pdimens
closed
2 months ago
0
100 impute create separate conda env for stitch
#101
pdimens
closed
2 months ago
0
[IMPUTE] create separate conda env for STITCH
#100
pdimens
closed
2 months ago
1
alphabetize workflow options
#99
pdimens
closed
2 months ago
0
[QC] --skip-adapters should be opt-in as --trim-adapters
#98
pdimens
closed
2 months ago
0
[QC] add deduplication to fastp
#97
pdimens
closed
2 months ago
0
[internal] replace --print-only with --config-only
#96
pdimens
closed
2 months ago
0
Docs 1.1
#95
pdimens
closed
2 months ago
0
replace molecule distance with QuickDeconvolute?
#94
pdimens
closed
2 months ago
0
move pysam into main env
#93
pdimens
closed
2 months ago
0
Add aggregate report for bx stats
#92
pdimens
closed
2 months ago
0
add pysam as direct dependency
#91
pdimens
closed
2 months ago
0
replace minimap with strobealign
#90
pdimens
closed
2 months ago
0
replace minimap with strobealign
#89
pdimens
closed
2 months ago
0
new input model listing abspaths in config.yaml
#88
pdimens
closed
2 months ago
0
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