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KwanLab
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Autometa
Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
https://autometa.readthedocs.io
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helpful error message added
#307
RajnishProgrammer
closed
10 months ago
1
Add helpful error message
#306
chasemc
opened
1 year ago
1
Propagate contigs not recovered in blastp search to `unclassified.fna`
#305
evanroyrees
closed
10 months ago
0
Documentation needs edit
#304
chasemc
opened
1 year ago
0
:snake: Replace `attrs` with `dataclasses`
#303
evanroyrees
opened
1 year ago
0
🐍 ⬆️ Add snakemake workflow file
#302
Sidduppal
closed
10 months ago
4
Replace prodigal subprocess with pyrodigal
#301
evanroyrees
opened
1 year ago
0
Release 2.2.0
#300
evanroyrees
closed
1 year ago
1
Release 2.2.0
#299
evanroyrees
closed
1 year ago
1
error: archaea.markers.tsv not found
#298
Valentin-Bio-zz
opened
1 year ago
2
Problem when running Autometa using bash script
#297
Valentin-Bio-zz
closed
1 year ago
6
The number of contigs after autometa-taxonomy is not consistent to the original contig fasta
#296
chtsai0105
closed
10 months ago
5
Error occurred on running autometa-binning
#295
chtsai0105
closed
1 year ago
2
test pull request for myst-formatted documentation
#294
kaw97
closed
1 year ago
1
Documentation
#293
kaw97
closed
1 year ago
1
Improvements/bug fixes in mock data workflow
#292
chasemc
closed
1 year ago
5
Running the test profile fails, unable to find docker image
#291
chasemc
opened
1 year ago
0
Add `--average-method` parameter to `autometa-benchmark`
#290
evanroyrees
closed
1 year ago
2
Add `average_method` argument to `compute_clustering_metrics` function
#289
evanroyrees
closed
1 year ago
0
No clusters can be found in the dataset
#288
ReneKat
closed
1 year ago
4
🐌 ➡️ 🐎 Optimize DBSCAN clustering method for genome binning
#287
evanroyrees
opened
1 year ago
0
force scipy==1.8
#286
kaw97
closed
1 year ago
1
Pin scipy release to `1.8.*` until scikit-bio uses scipy 1.9
#285
evanroyrees
closed
1 year ago
0
⬆️ 🎨 Allow the use of gtdb taxonomy in Autometa
#284
Sidduppal
closed
1 year ago
10
Allow the use of gtdb taxonomy in Autometa
#283
Sidduppal
closed
1 year ago
2
FileNotFoundError: [Errno 2] No such file or directory: '/databases/autometa/ncbi/delnodes.dmp'
#282
JoshuaTCooper
closed
2 years ago
1
New bash files for Autometa workflow
#281
samche42
closed
1 year ago
1
:shell: Add feature: New batch file scripts for documentation
#280
samche42
closed
2 years ago
3
:art::snake: Update deprecated pandas method invocation
#279
evanroyrees
closed
2 years ago
2
Documentation update
#278
jason-c-kwan
closed
10 months ago
2
:memo: Added contribution documentation
#277
jason-c-kwan
closed
2 years ago
1
:art::snake: Add CAMI formatter entrypoint `autometa-cami-format`
#276
evanroyrees
closed
2 years ago
2
Print commands run in context in autometa.sh script
#274
kirstengott
closed
2 years ago
2
Release 2.1.0
#273
evanroyrees
closed
2 years ago
2
:bug::shell: Fix variable name for autometa-binning-summary
#272
evanroyrees
closed
2 years ago
1
:art::green_apple: Add `autometa --version` to autometa nextflow files
#271
evanroyrees
closed
2 years ago
1
Versioning
#269
evanroyrees
closed
2 years ago
2
General Query on improvising Metagenome binning
#268
srisvs33
closed
2 years ago
6
:art::bug::snake: Add `n_jobs` to `embed(...)` func. Replace `**method_args` w/ `**method_kwargs`
#267
evanroyrees
closed
2 years ago
1
:bug::snake: Add `n_jobs` argument to `kmers.embed(...)` function and replace `**method_args`
#266
evanroyrees
closed
2 years ago
0
:snake::bug: Fix parsing taxids to delnodes set
#265
evanroyrees
closed
2 years ago
2
:arrow_up: :green_apple: Upgrade Diamond 2.0.9 -> 2.0.14
#264
chasemc
closed
2 years ago
1
Add threads for for bowtie2-build
#263
chasemc
opened
2 years ago
0
:memo: Update installation directions for bash workflow
#262
evanroyrees
closed
2 years ago
1
Missing step in documentation (Bash workflow)
#261
jason-c-kwan
closed
2 years ago
0
:art::snake: Add taxid conversion from `'unclassified'` to `1` for taxon-profiling benchmarking
#260
evanroyrees
closed
2 years ago
2
Release 2.0.3
#259
evanroyrees
closed
2 years ago
1
Check NCBI connection instead of pinging google DNS
#258
ajlail98
closed
2 years ago
2
internet_is_connected() function
#257
paulineauffret
closed
2 years ago
4
:art::bug::snake: Fix `autometa-length-filter` bug when `--output-fasta` is specified without an output directory
#256
evanroyrees
closed
2 years ago
2
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