lauralwd/Azolla_genus_metagenome
This project aims do describe and explore the metagenomes of fern species of the genus Azolla.
PythonGPL-3.0
Issues
- 0
checkm optimisation
#49 opened by lauralwd - 0
- 0
- 0
explicitly remove or compress output files in the assembly folders to slim down the project
#46 opened by lauralwd - 0
- 0
remove binningsignal folders after succesfuly completing SNV detection in Anvio to slim down the project
#44 opened by lauralwd - 0
compress CAT tables by default
#43 opened by lauralwd - 1
- 4
introduce hybrid assemblies
#41 opened by lauralwd - 1
- 3
- 0
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clarify and/or correct rule names.
#17 opened by lauralwd - 0
split huge snakemake file in smaller files
#33 opened by lauralwd - 2
- 1
samtools doesn't log propperly
#37 opened by lauralwd - 1
Use both dedicated binning signals and sequencing reads used for assembly as input signals for binning
#19 opened by lauralwd - 3
- 1
use chloroplast genome for filtering as well. Implement chloroplast download rule and a rule to merge it into the filterfasta file.
#31 opened by lauralwd - 1
- 6
adapt CAT settings for better annotation
#27 opened by lauralwd - 0
- 0
implement shadow directive in CAT rules
#21 opened by lauralwd - 0
Host orfs plant specific in a separate rule
#28 opened by lauralwd - 0
readme needs update
#25 opened by lauralwd - 1
CAT naming produces inconsistent columns when I read the output as a table in R. implement the CAT --only_official option and evaluate whether output is better readable
#16 opened by lauralwd - 2
Allow for failed SPAdes runs to keep (part) of the files and resume with more memory rather than starting over.
#5 opened by lauralwd - 0
rule shorten scaffold_names: fix awk onliner
#10 opened by lauralwd - 0
- 0
- 1
get extra samples for binning signal
#3 opened by lauralwd - 0
Separate SPAdes-hmmer from assembly for 1: more clarity in the DAG graph, and 2: easy reuse of error corrected files after failed assemblies.
#6 opened by lauralwd - 0
- 0