dib-lab charcoal issues

dib-lab / charcoal

Remove contaminated contigs from genomes using k-mers and taxonomies.

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[MRG] update sourmash and snakemake versions

#190 ctb closed 3 years ago
0
Eukaryotic genome providing lineages?

#189 ilikvlad opened 3 years ago
6
[MRG] Fix `all_clean_contigs` target for short contigs

#188 ctb closed 3 years ago
6
I think `charcoal run` defaults to target `report` w/o being told to run it

#187 taylorreiter opened 3 years ago
0
KeyError in charcoal target `all_clean_contigs`

#186 taylorreiter closed 3 years ago
5
charcoal target `clean` does not work

#185 taylorreiter opened 3 years ago
1
feedback/brainstorm for refining charcoal reports

#184 taylorreiter opened 3 years ago
0
[MRG] update snakemake and other dependencies

#183 ctb closed 3 years ago
3
Snakemake --conda-frontend conda error (mamba package not available)

#182 ilikvlad opened 3 years ago
6
segfault in mashmap compare on empty input files

#181 taylorreiter closed 3 years ago
5
[MRG] flatten db sigs for in contam code

#180 taylorreiter closed 3 years ago
4
[MRG] add code to remove duplicate prefetch matches when db has duplicate signatures

#179 taylorreiter closed 3 years ago
0
[MRG] flatten mh to allow gather_at_rank

#178 taylorreiter closed 3 years ago
7
charcoal `TypeError` in rule `make_contigs_taxonomy_json` with abundance signature

#177 taylorreiter closed 3 years ago
1
[MRG] update to sourmash v4.1.1

#176 ctb closed 3 years ago
0
built in workaround for sigs that are in the db?

#175 taylorreiter closed 3 years ago
13
`gather_at_rank` handling ties in taxonomic assignment

#174 taylorreiter opened 3 years ago
0
add test for `just_taxonomy` file handle

#173 taylorreiter opened 3 years ago
0
[MRG] Fix tests for #171

#172 ctb closed 3 years ago
0
[MRG] update to sourmash 4.1.0

#171 taylorreiter closed 3 years ago
11
[WIP] fix a few things in the demo

#170 ctb closed 3 years ago
2
Errors when doing the full configure & run with the 10 MAGs from Delmont et al.

#169 edgraham closed 3 years ago
1
Demo fails due to missing rule exception in Snakemake

#168 edgraham closed 2 years ago
1
Demo fails (on Mac)

#167 phiweger opened 3 years ago
4
alignplot- missing dependencies and error message

#166 clmattson-zz opened 3 years ago
1
add direct nucmer and mashmap subcommands to alignplot

#165 ctb opened 3 years ago
0
Add alignment post-processing for stage2.

#164 ctb closed 3 years ago
0
Add contig filter-by-query-bases-covered; refactor to stage1, stage2, etc.

#163 ctb closed 3 years ago
0
next steps for charcoal - some thoughts

#162 ctb opened 3 years ago
2
Refactor alignplot.py

#161 ctb closed 3 years ago
0
Prepare charcoal for doing actual alignments against actual genomes

#160 ctb closed 3 years ago
0
Add GitHub actions

#159 ctb closed 3 years ago
1
Another large refactoring, this time with direction and purpose.

#158 ctb closed 3 years ago
0
Attempts to update #150 after my other merges

#157 ctb opened 3 years ago
0
Fix tests

#156 ctb closed 3 years ago
0
Experiments in exploring the taxonomy of contaminants, mark 2. (#149)

#155 ctb closed 3 years ago
0
can we use greyhound or MAGsearch to identify/correlate/analyze contamination?

#154 ctb opened 4 years ago
1
use csvtk concat to combine CSVs

#153 ctb closed 3 years ago
1
Error in rule make_contigs_taxonomy_json (full configure and run)

#152 RoyHerVel opened 4 years ago
2
single query contamination - more brainstorming

#151 ctb opened 4 years ago
5
conduct contig and genome gathers together to avoid rebuilding LCA

#150 bluegenes opened 4 years ago
0
Experiments in exploring the taxonomy of contaminants, mark 2.

#149 ctb closed 3 years ago
0
multi-stage charcoal?

#148 ctb opened 4 years ago
0
provide example configurations in documentation

#147 ctb opened 4 years ago
0
use case: comparing contamination due to assembler used

#146 ctb opened 4 years ago
0
use metagenome search for validating results?

#145 ctb opened 4 years ago
2
Experiments in exploring the taxonomy of contaminants.

#144 ctb closed 4 years ago
2
speed up / parallelize `compare_taxonomy` step

#143 ctb opened 4 years ago
1
Update summary output with treemaps.

#142 ctb closed 4 years ago
0
provide space for user notes and comments on genomes

#141 ctb opened 4 years ago
0

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