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MrOlm
/
inStrain
Bioinformatics program inStrain
MIT License
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Troubleshooting inStrain profile Step 2. Profile scaffolds
#141
jmartin77777
closed
1 year ago
3
samtools left out of v1.7.1 pip installation
#140
rrohwer
closed
1 year ago
1
Error trying to install pysam when installing instrain
#139
dzjian2
closed
1 year ago
3
-mb minimum breadth option in inStrain plot
#138
BenLRoss
closed
1 year ago
2
pNpS calculations
#137
Riiiiiis
closed
1 year ago
9
Dendrogram colours
#136
adijatj
closed
1 year ago
1
Can we use inStrain profile results (e.g. popANI, conANI) to decide if two genomes belong to the same strain?
#135
JemmaSun
closed
1 year ago
1
making plots is failing although everything else finishes without error
#134
rrohwer
closed
1 year ago
6
instrain compare on multiple profiles
#133
adijatj
closed
1 year ago
5
conda/pip installations need phython <3.11
#132
rrohwer
closed
1 year ago
2
retrieving data underneath plot #3 - read ANI distribution
#131
mcmahon-uw
closed
1 year ago
2
missing genomes in genome_info.tsv files.
#130
jehaab
closed
1 year ago
2
Update README.md
#129
alexcritschristoph
closed
1 year ago
1
Compare does not create plot 10
#128
marotbone
closed
1 year ago
4
Trouble installing inStrain with Conda
#127
alipirani88
closed
1 year ago
2
The parameter --skip_mm_profiling has an impact in the accurary of the variant calling step?
#126
gabrieleghiotto
closed
1 year ago
6
Is this method applicable to eukaryotes？
#125
haihao999
closed
1 year ago
1
instrain profile flag "min_read_ani" not working?
#124
mcmahon-uw
closed
1 year ago
2
to include or remove plasmids in reference genome databases?
#123
brittanysuttner
closed
1 year ago
1
FileNotFoundError: [Errno 2] No such file or directory: 'samtools'
#122
LeahBriscoe
closed
1 year ago
2
Suppress Pandas FutureWarning
#121
vinisalazar
closed
1 year ago
1
Question about instrain
#120
SilasK
closed
1 year ago
5
inStrain compare: AssertionError: No scaffolds are shared amoung the IS
#119
celine77
closed
1 year ago
13
Use bining data as ref-genome
#118
BaylorLyu
closed
1 year ago
2
Problem of false positive SNVs
#117
gabrieleghiotto
closed
1 year ago
2
Best practice to compare hundreds of samples
#116
zhaoc1
closed
1 year ago
2
FutureWarning message of v1.6.3.
#115
zhaoc1
closed
1 year ago
2
Minor issue with argument orders for inStrain profile
#114
ryanmelnyk
closed
2 years ago
1
ModuleNotFoundError: No module named 'numba'`
#113
mcmahon-uw
closed
1 year ago
2
Question about non-synonymous/synonymous mutation calculations when gene is on the negative strand
#112
szimmerman92
closed
2 years ago
3
Bug fix for generating pooled snv tables and adding progress bar for generating tables
#111
szimmerman92
closed
2 years ago
0
position in scaffold
#110
guyuanl
closed
2 years ago
2
inStrain compare key error when SNV Pooling
#109
szimmerman92
closed
2 years ago
4
Question: SNVs shared across samples
#108
cifuj
closed
2 years ago
1
Tutorial 1 comparison error
#107
iwilkie
closed
2 years ago
14
Issue of "I dont know how to process ... (the gene file)"
#106
ChaoLab
closed
2 years ago
5
Can Instrain differentiate between read_ids for paired-end file in bam file?
#105
kaysahu
closed
2 years ago
2
InStrain for PacBio longreads
#104
DanielSpari
opened
2 years ago
3
The question for running command "inStrain profile"
#103
toggle0511
opened
2 years ago
4
null model seems not being consistently applied leading to wrong allelle_counts
#102
zhaoc1
closed
2 years ago
5
multiprocessing error
#101
y-hwang
closed
2 years ago
3
Minimum files for compare
#100
kirkgrubbs1
closed
2 years ago
3
Coverage discrepancy with inStrain profile
#99
cswift3
opened
2 years ago
6
Distributing Comparisons
#98
kirkgrubbs1
closed
2 years ago
11
inStrain compare gives "You're comparing ISP profiles that have the same names." message
#97
jdwinkler-lanzatech
closed
2 years ago
3
allele frequency
#96
YongyiPeng
closed
2 years ago
2
inStrain compare not printing strain_clusters.tsv
#95
clb21565
closed
2 years ago
4
Pass input profiles in text file to inStrain compare
#94
jdwinkler-lanzatech
opened
2 years ago
2
Estimating number of strains based on nucleotide diversity, pop ANI, number of SNVs
#93
gabrieleghiotto
closed
2 years ago
1
Insights regarding nucleotide diversity vs SNVs
#92
DDavila10
opened
2 years ago
4
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