apcamargo/genomad issues and pull requests

#133 - Results are different between different runs

Issue - State: closed - Opened by chenyj8 6 days ago - 5 comments

#132 - how to transform the output _taxonomy.tsv file into sample level mpa file?

Issue - State: open - Opened by joelive 17 days ago - 3 comments

#131 - run failed during annotation

Issue - State: open - Opened by mikenada 19 days ago - 1 comment

#130 - The letter M exists in the viral genome

Issue - State: open - Opened by lsj-666 21 days ago - 1 comment

#129 - Unable to install genomad on HPC

Issue - State: closed - Opened by sadia-marjia 25 days ago - 1 comment

#128 - sample-based assemblies vs merged?

Issue - State: closed - Opened by mhmism about 2 months ago - 3 comments

#127 - Genomad license in Galaxy tools

Issue - State: open - Opened by bernt-matthias about 2 months ago - 5 comments

#126 - Usage of score calibration

Issue - State: open - Opened by zehanna 2 months ago - 5 comments

#125 - cut-off point for plasmid_score

Issue - State: closed - Opened by p-suazo-soto 2 months ago - 7 comments

#124 - Identification of plasmids in main contig

Issue - State: open - Opened by Kir283 2 months ago - 1 comment

#123 - antonio is busy

Pull Request - State: open - Opened by UriNeri 2 months ago

#122 - Question about use of calibrated aggregation scores

Issue - State: open - Opened by gweeenis 3 months ago - 1 comment

#121 - Question on fundamentals

Issue - State: open - Opened by songmj86 3 months ago - 1 comment

#120 - line 19 in aggregated_classfication.py

Issue - State: open - Opened by caojy-sys 3 months ago - 2 comments

#119 - Discrepancy in Output Counts in Genomad

Issue - State: open - Opened by F4NG666 3 months ago - 1 comment

#118 - Chromosome classification result

Issue - State: closed - Opened by LeabaeL 3 months ago - 2 comments

#117 - Number of contigs in the assembly

Issue - State: open - Opened by coreyholt 3 months ago - 1 comment

#116 - How to export the viral DNA gene sequence?

Issue - State: open - Opened by wfgui 4 months ago - 5 comments

#115 - question about integrase identification during provirus identification

Issue - State: closed - Opened by mujiezhang 4 months ago - 3 comments

#114 - Genetic codes

Issue - State: closed - Opened by Khalimat 4 months ago - 2 comments

#113 - Error mmseqs prefilter

Issue - State: closed - Opened by brilliant2643 4 months ago - 2 comments

#112 - Provirus detection in genomad vs checkv

Issue - State: closed - Opened by lingrongjin 4 months ago - 6 comments

#111 - The question about --disable-nn-classification

Issue - State: open - Opened by ZoeLct 4 months ago - 1 comment

#110 - Fewer viral contigs identified from genomad vs virsorter2

Issue - State: closed - Opened by lingrongjin 5 months ago - 4 comments

#109 - Optimization Request for Analyzing Large Number of MAGs with geNomad

Issue - State: closed - Opened by Songfengl 5 months ago - 5 comments

#108 - plasmid classified as virus?

Issue - State: open - Opened by xinehc 5 months ago - 7 comments
Labels: enhancement, good first issue

#107 - genomad annotate fastq file is empty or contains multiple entries

Issue - State: open - Opened by skose82 5 months ago - 3 comments

#106 - Error mmseqs prefilter

Issue - State: closed - Opened by namnh7 5 months ago - 4 comments

#105 - Error while classifying sequences

Issue - State: open - Opened by LCFortier 5 months ago - 9 comments

#104 - Small (reference) data for testing

Issue - State: closed - Opened by bernt-matthias 6 months ago - 9 comments

#103 - Different protein number from genomad and pyrodigal-gv

Issue - State: closed - Opened by quliping 6 months ago - 2 comments

#102 - mmseqs2 error

Issue - State: closed - Opened by manaraleslam2018 6 months ago - 3 comments

#101 - Error with geNomad v1.8.0, missing tensorflow.keras

Issue - State: closed - Opened by flefler 6 months ago - 8 comments

#100 - geNomad taxonomy about Baltimore classification

Issue - State: open - Opened by xjhzjucas 7 months ago - 1 comment

#99 - The virus identified by genomad weren't annotated as virus sequence by VIBRANT?

Issue - State: open - Opened by Caiyulu-818 7 months ago - 3 comments

#98 - Errors when download and the same issue when running genomad -h

Issue - State: closed - Opened by Tsingsjeen 7 months ago - 3 comments

#97 - AMR annotations on chromsome?

Issue - State: open - Opened by sophiaaredas 7 months ago - 1 comment

#96 - Whether measures have been taken by genomad to avoid identifying genomic islands as viruses?

Issue - State: closed - Opened by ZongzhiWu 7 months ago - 5 comments

#95 - [feature request] query database clustering

Issue - State: open - Opened by valentynbez 7 months ago - 1 comment
Labels: enhancement, good first issue

#94 - Inquiry on virus from MAG

Issue - State: closed - Opened by songmj86 7 months ago - 4 comments

#93 - Error downloading database

Issue - State: open - Opened by simeonhebrew 7 months ago - 4 comments

#92 - Circular virus identification

Issue - State: closed - Opened by xjhzjucas 7 months ago - 5 comments

#91 - Recommendations for subsampling BIG input file

Issue - State: closed - Opened by wyanren 7 months ago - 1 comment

#90 - Database download does not work

Issue - State: closed - Opened by joao1980 8 months ago - 1 comment

#89 - License request

Issue - State: open - Opened by Amanda-Biocortex 8 months ago - 1 comment

#88 - Error with geNomad

Issue - State: closed - Opened by xjhzjucas 8 months ago - 7 comments

#87 - Interpretation of results - plasmids with 0 genes?

Issue - State: closed - Opened by jimen210 8 months ago - 7 comments
Labels: enhancement

#86 - Can we input virus(phage) sequences to identify the plasmid sequence in the virus sequence?

Issue - State: closed - Opened by Caiyulu-818 8 months ago - 5 comments

#85 - Recommendation for taxonomic classification of ssDNA virus

Issue - State: closed - Opened by ChenTianYi99 8 months ago - 5 comments

#84 - Support Keras 3

Issue - State: open - Opened by apcamargo 8 months ago

#83 - ValueError: Cannot convert '5997' to a shape.

Issue - State: closed - Opened by WUD2018 8 months ago - 3 comments

#82 - virus taxonomy only

Issue - State: closed - Opened by Caiyulu-818 9 months ago - 1 comment

#80 - genomad hangs

Issue - State: closed - Opened by erinyoung 9 months ago - 2 comments

#79 - High discrepancy between the high amount of viruses for geNomad and the low number of complete viruses

Issue - State: open - Opened by bhagavadgitadu22 9 months ago - 5 comments

#78 - Error at NN step when trying to process a single sample

Issue - State: closed - Opened by simroux 9 months ago - 16 comments

#77 - Questions about geNomad

Issue - State: closed - Opened by lsj-666 9 months ago - 7 comments

#76 - CLI option to set output prefix

Issue - State: open - Opened by zclaas 9 months ago - 1 comment
Labels: enhancement

#75 - Inconsistency in number of genomes reported by genomad

Issue - State: closed - Opened by valentynbez 10 months ago - 7 comments

#74 - Several questions about geNomad

Issue - State: closed - Opened by xjhzjucas 10 months ago - 2 comments

#73 - How to run genomad on only complete sequences (DTR or ITR)?

Issue - State: open - Opened by ZongzhiWu 10 months ago - 1 comment

#72 - How IMG/PR database used in genomad

Issue - State: closed - Opened by Dx-wmc 10 months ago - 4 comments

#71 - Provide prediction intervals

Issue - State: open - Opened by apcamargo 11 months ago
Labels: enhancement

#70 - Purpose of the `BranchAttention` class in `igloo.py`

Issue - State: closed - Opened by a-piece-of-teemo 11 months ago - 1 comment

#69 - Could you please explain the functions of these files？

Issue - State: closed - Opened by a-piece-of-teemo 11 months ago - 1 comment

#68 - How to further develop on the basis of your code

Issue - State: closed - Opened by zzzfire 11 months ago - 3 comments

#67 - Unable to download database v1.7.4

Issue - State: closed - Opened by SCWang429 11 months ago - 3 comments

#66 - Include empty fields in taxonomy for easier parsing

Pull Request - State: closed - Opened by LanderDC 11 months ago - 6 comments

#65 - undefined symbol error in end-to-end pipeline

Issue - State: open - Opened by DOieGYuan 11 months ago - 5 comments

#64 - How are the weights matrices calculated in the aggregated classification module？

Issue - State: closed - Opened by a-piece-of-teemo 11 months ago - 10 comments

#63 - The xgboost model in the code and how to train the xgboost model

Issue - State: closed - Opened by ZoeLct 11 months ago - 1 comment

#62 - Sorry I have one more question

Issue - State: closed - Opened by songmj86 11 months ago - 3 comments

#61 - Inquiry on threshold

Issue - State: closed - Opened by songmj86 11 months ago - 2 comments

#60 - Feature request: GBK/GFF as input

Issue - State: open - Opened by alexweisberg 11 months ago - 2 comments

#59 - How should genomad be used appropriately, when there are a huge number of assemblies to be processed.

Issue - State: open - Opened by actledge 12 months ago - 1 comment

#58 - The integrase on prophages and other viruses issue

Issue - State: closed - Opened by ChaoLab 12 months ago - 8 comments

#57 - Marker classfication and other stuff

Issue - State: closed - Opened by AhmedElsherbini 12 months ago - 6 comments

#56 - KeyError: 'ATAACA' happened in Executing genomad marker-classification.

Issue - State: closed - Opened by YANG-Jiwei 12 months ago - 9 comments

#55 - [Question] Taxonomy on a viral bin with multiple contigs

Issue - State: closed - Opened by jolespin 12 months ago - 1 comment

#54 - cudnn error in nn-classification

Issue - State: closed - Opened by pck00 12 months ago - 3 comments

#53 - error with end-to-end

Issue - State: open - Opened by abdo3a about 1 year ago - 5 comments

#52 - Does geNomad currently support training new models?

Issue - State: closed - Opened by a-piece-of-teemo about 1 year ago - 10 comments

#51 - Unable to run

Issue - State: open - Opened by WenluYIN about 1 year ago - 4 comments

#50 - Error running Genomad 1.7.1

Issue - State: open - Opened by mhmism about 1 year ago - 2 comments

#49 - Take circularity into account when applying post-classification filters

Issue - State: open - Opened by apcamargo about 1 year ago

#48 - Support for GFF and GBK outputs

Issue - State: open - Opened by apcamargo about 1 year ago
Labels: enhancement

#47 - Finding chimeric sequences

Issue - State: closed - Opened by bhimbbiswa about 1 year ago - 4 comments

#46 - Step skipping doesn't work properly in the classification modules when the output of `annotate` changes

Issue - State: open - Opened by apcamargo about 1 year ago

#45 - Interpretation of Results

Issue - State: closed - Opened by owbarber about 1 year ago - 3 comments

#44 - Fasta contains multiple entries with the same identifier

Issue - State: closed - Opened by jsming1996 about 1 year ago - 1 comment

#43 - Issues running genomad

Issue - State: open - Opened by david1ibarra about 1 year ago - 1 comment

GitHub / apcamargo/genomad issues and pull requests