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shenwei356
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kmcp
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
https://bioinf.shenwei.me/kmcp
MIT License
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Merge kmcp profilings of multiple samples
#45
DrYoungOG
opened
3 weeks ago
2
How to profile results only identify 1 species per reference
#44
nvhphuc1206
opened
3 months ago
6
kmcp search is stucked
#43
aababc1
closed
4 months ago
4
coverage is greater than 100
#42
wz115
opened
7 months ago
1
Availability of old gtdb databases?
#41
fplazaonate
closed
7 months ago
5
TODO: save the search result into a serializing binary file for fast downstream parsing
#40
shenwei356
opened
10 months ago
3
Kmcp profile empty
#39
sofstam
closed
10 months ago
2
Optimizing KMCP with HumGut
#38
ericvdtoorn
opened
10 months ago
9
Merge error (number of fields < query index field)
#37
ericvdtoorn
closed
9 months ago
3
ETA missing when building KMCP index
#36
ericvdtoorn
closed
9 months ago
4
[Suggestion] Use score calibration when identifying proviruses and plasmids
#35
apcamargo
opened
11 months ago
2
KMCP's MetaPhlAn output doesn't follow the MetaPhlAn file format
#34
apcamargo
closed
9 months ago
3
Report statistics of matched, unmatched reads
#33
shenwei356
closed
11 months ago
1
Detecting closest reference in custom DB
#32
jodyphelan
closed
1 year ago
4
Add a tutorial of detecting specific pathogen in sequencing data
#31
shenwei356
closed
11 months ago
1
How to specify multiple kmer values
#30
mbhall88
closed
1 year ago
2
Masking prophages in bacterial genomes before building database as Phanta does
#29
shenwei356
opened
1 year ago
2
suitable for CDS and/or contig taxonomic assignment?
#28
AstrobioMike
opened
1 year ago
2
long read metagenomic profiling
#27
JensUweUlrich
opened
1 year ago
2
Dealing with novel/non-sequenced species
#26
mverce
closed
1 year ago
2
KMCP database building tutorial
#25
Cryphonectria
closed
1 year ago
3
CowTransfer link doesn't work
#24
jamelee
closed
1 year ago
3
kmcp search is very slow for metatranscriptome data
#23
shenwei356
closed
1 year ago
6
Profiling output table interpretation
#22
lborcard
closed
1 year ago
3
Estimating abundance using EM algorithm
#21
shenwei356
closed
1 year ago
0
reporting proportion of unmatched reads
#20
peterbjarke
closed
1 year ago
4
0.8.3: Fails on i386: 1 << 32 - 1 (untyped int constant 4294967295) overflows int
#19
yurivict
closed
1 year ago
4
Create an index without create the database
#18
davidmaimoun
closed
1 year ago
4
compiling/installing from source
#17
jianshu93
closed
1 year ago
9
Error when installing KMCP
#16
davidmaimoun
closed
2 years ago
9
QUESTION: Taxdump
#15
alienzj
closed
1 year ago
2
QUESTION: KMCP merge
#14
alienzj
closed
2 years ago
4
Automatically disable ambiguous-matches correction for complex communities with thousands of species
#13
shenwei356
opened
2 years ago
0
Building database with MAGs
#12
durrantmm
closed
2 years ago
2
TODO: support viral genomes collections, e.g, MGV, GPD
#11
shenwei356
closed
1 year ago
3
kmcp search crashed
#10
zhanxw
closed
1 year ago
5
[website] broken links
#9
telatin
closed
2 years ago
1
A minor issue on console messages
#8
zhanxw
closed
2 years ago
3
profile: decrease thresholds of minimal reads and unique reads in preset profiling modes 1 and 2 for low coverage sequence data
#7
shenwei356
closed
2 years ago
0
TODO: improve search results parsing by using a simplified version of strconv.ParseFloat
#6
shenwei356
closed
2 years ago
1
TODO: allow changing parts of the parameters for preset profiling modes
#5
shenwei356
closed
2 years ago
0
Metaphlan format profile report file seems to lack NCBI taxonomy IDs.
#4
ilnamkang
closed
2 years ago
3
Read-level output format
#3
sjaenick
closed
2 years ago
1
support multiple sizes of k-mer
#2
shenwei356
closed
3 years ago
0
Support multiple set membership testing (MSMT) from RAMBO
#1
shenwei356
closed
3 years ago
0