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polio-nanopore
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piranha
GNU General Public License v3.0
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Name suggestions for bioconda recipe
#89
rpetit3
closed
1 year ago
6
allow multiple neg/pos controls per sample
#88
aineniamh
closed
10 months ago
0
no-temp info in readme
#87
aineniamh
closed
1 year ago
0
bcode report embedded seqs
#86
aineniamh
closed
1 year ago
1
flag for env or stool sample
#85
aineniamh
closed
1 year ago
0
general disclaimer about wpv3 etc in manual
#84
aineniamh
closed
1 year ago
0
flag change to env samples only, and only if a few polio reads- also do a proportion rather than a count
#83
aineniamh
closed
1 year ago
0
Qc addition
#82
aineniamh
closed
1 year ago
0
Read count without sp switch
#81
aineniamh
closed
1 year ago
0
write a vignette or manual or similar
#80
aineniamh
closed
1 year ago
0
qc for contaminants
#79
aineniamh
closed
1 year ago
0
additional metadata in output fasta file
#78
aineniamh
closed
1 year ago
0
QC to be added
#77
aineniamh
closed
1 year ago
1
install on fresh mac
#76
aineniamh
closed
1 year ago
0
installation instructions note i should type ‘git clone https://github.com/aineniamh/piranha.git && cd piranha’ – should this be updated to ‘git clone https://github.com/polio-nanopore/piranha.git && cd piranha’?
#75
aineniamh
closed
1 year ago
1
example report still gives ‘file not found’ 404
#74
aineniamh
closed
1 year ago
1
embed seqs in file
#73
aineniamh
closed
1 year ago
0
table with identical seqs mentioned
#72
aineniamh
closed
1 year ago
0
test m1 with following:
#71
aineniamh
closed
1 year ago
1
adding gzip compatibility for issue #64
#70
aineniamh
closed
1 year ago
0
whole genome configuration for single amplicon
#69
aineniamh
closed
1 year ago
1
properly embed the fasta file so the report doesn't need relative path consistency
#68
aineniamh
closed
1 year ago
0
website for poseco with links to resources and logos
#67
aineniamh
closed
1 year ago
0
Read Counts in Report exceed read counts in input file
#66
DarianHole
closed
1 year ago
4
automated docker image with new release
#65
aineniamh
closed
1 year ago
0
accept gz files as input too
#64
aineniamh
closed
1 year ago
0
Seq raw data fastq bins
#63
aineniamh
closed
1 year ago
0
Analytical update
#62
aineniamh
closed
1 year ago
0
French dev
#61
aineniamh
closed
1 year ago
0
call variation info vs new cns in non sabin seqs
#60
aineniamh
closed
1 year ago
0
cooccurance haplotype assessment
#59
aineniamh
closed
1 year ago
0
look at using varialabel
#58
aineniamh
closed
1 year ago
0
{pore}_{device}_{caller variant}_{caller version} option
#57
aineniamh
closed
1 year ago
1
test m1 installation
#56
aineniamh
closed
1 year ago
1
resource allocation, mem requirements, speed, accuracy medaka vs nanopolish
#55
aineniamh
closed
1 year ago
0
sample ids replace spaces with underscores, with a warning
#54
aineniamh
closed
2 years ago
1
make it an explicit protocol instead of just wg or vp1
#53
aineniamh
closed
2 years ago
1
pan ev and wg
#52
aineniamh
closed
1 year ago
0
recombination and whole genome
#51
aineniamh
opened
2 years ago
1
nanopolish as a potential inference option
#50
aineniamh
closed
2 years ago
0
Legend testing
#49
aineniamh
closed
2 years ago
0
highlight vdpv in landing table
#48
aineniamh
closed
1 year ago
0
update flag
#47
aineniamh
closed
1 year ago
1
explicitly handle homopolymer site at 50bp in sabin2
#46
aineniamh
closed
1 year ago
1
french version of report
#45
aineniamh
closed
1 year ago
0
optional reference database
#44
aineniamh
closed
2 years ago
1
wg pipeline
#43
aineniamh
closed
2 years ago
1
For wt, don't need to list or show all snps relative to the nearest wt sequence- just have the actual fasta seq there
#42
aineniamh
closed
2 years ago
0
configurable where all new cns from a particular run gets pushed to
#41
aineniamh
closed
1 year ago
0
wt pv, map against single ref vs wholedatabase- how does this affect num of reads mapping
#40
aineniamh
closed
1 year ago
0
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