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snayfach
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MIDAS
An integrated pipeline for estimating strain-level genomic variation from metagenomic data
http://dx.doi.org/10.1101/gr.201863.115
GNU General Public License v3.0
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no outputs for speciation
#135
qinghong2019
opened
1 year ago
0
Update tutorial.md
#134
snayfach
closed
1 year ago
0
cannot download the database midas_db_v1.2.tar.gz
#133
qinghong2019
closed
1 year ago
2
Population diversity with intermediate frequency
#132
azk001
closed
1 year ago
1
Request for information on how are marker genes chosen in custom database ?
#131
Aiswarya-prasad
closed
2 years ago
4
test_class (__main__._07_RunSNPs) ... FAIL
#130
Daisyiscool
opened
2 years ago
0
Question regarding speed of execution
#129
rdauria
opened
2 years ago
1
AttributeError: Can't pickle local object 'parallel.<locals>.init_worker'
#128
thapasz
closed
2 years ago
1
How can I use MIDAS to get pN/pS on a per-gene basis?
#127
JuliaMcGonigle
opened
2 years ago
0
Samtools missing binaries
#126
kaysahu
opened
2 years ago
3
samtools errors
#125
tbazilegith
opened
2 years ago
1
build custom database error
#124
wangxgong
opened
3 years ago
0
samtools invalid option 'f'
#123
aflynncarroll
opened
3 years ago
0
Database marker gene file "phyeco.map" has wrong genome_id label
#122
zeqianli
opened
3 years ago
0
samtools check updated to work in Batch mode
#121
slacalle
opened
3 years ago
1
Test 11 and 14 fails (and fixes)
#120
zeqianli
opened
3 years ago
0
Building database error
#119
JX-Zhong
opened
3 years ago
3
Can't download database
#118
zckoo007
opened
3 years ago
0
test_midas.py fail for test 7
#117
linzhouzz
opened
3 years ago
1
Strain tracking - getting identified strain names
#116
sanpande
opened
3 years ago
0
test not completing sucessfully
#115
sanpande
closed
3 years ago
1
setup.py: add scripts
#114
nick-youngblut
opened
3 years ago
0
flexible find exe
#113
nick-youngblut
opened
3 years ago
0
TypeError: cannot pickle '_io.TextIOWrapper' object
#112
Ivan-vechetti
opened
3 years ago
7
test_midas.py -vf test_class (__main__._07_RunSNPs) ... FAIL
#111
qiileee
closed
4 years ago
1
Error: could not execute bowtie2 binary
#110
BoyanZhou
opened
4 years ago
5
Link to database file is down
#109
7PintsOfCherryGarcia
closed
4 years ago
4
Conda Install
#108
JChristopherEllis
opened
4 years ago
5
Inconsistent species results
#107
mcleanlab
opened
4 years ago
0
Interpreting output from strain_tracking.py track_markers
#106
dadahan
opened
4 years ago
1
Strain tracking: identifying rare SNPs that discriminate individual strains
#105
dadahan
opened
5 years ago
0
Inclusion criteria for MAGs when setting up custom database
#104
adityabandla
opened
5 years ago
0
MIDAS build_midas_db.py issue
#103
allertm
closed
5 years ago
0
Boris/next
#102
boris-dimitrov
closed
5 years ago
0
Boris/pangenome
#101
boris-dimitrov
closed
5 years ago
0
Support for Pavian
#100
Anto007
opened
5 years ago
0
MIDAS is looking in the wrong place for 3rd party executables
#99
jolespin
opened
5 years ago
2
Strain tarcking and "marker alleles"
#98
VadimDu
opened
5 years ago
1
How to check which version of MIDAS is running?
#97
jolespin
opened
5 years ago
0
Boris/work 2018 02 05 b
#96
boris-dimitrov
closed
5 years ago
0
Boris/work 2019 02 05
#95
boris-dimitrov
closed
5 years ago
0
fix typos and use cpu_count for vsearch num threads
#94
boris-dimitrov
opened
5 years ago
0
Core-Genome Phylogenetic Trees with reference
#93
ilevade
opened
6 years ago
0
Annotations for merged geneIDs across samples
#92
drish91
opened
6 years ago
5
Adding to midas database?
#91
tamburinif
opened
6 years ago
3
genes with hundreds of copy number??
#90
biofuture
opened
6 years ago
0
test_midas.py -vf test_class (__main__._07_RunSNPs) ... FAIL
#89
biofuture
opened
6 years ago
3
Species detection threshold
#88
palomo11
closed
6 years ago
2
non-synonymous sites
#87
palomo11
closed
6 years ago
3
Bioconda bug
#86
thempatel
opened
6 years ago
7
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