lauralwd Azolla_genus_metagenome issues

lauralwd / Azolla_genus_metagenome

This project aims do describe and explore the metagenomes of fern species of the genus Azolla.

GNU General Public License v3.0

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checkm optimisation

#49 lauralwd opened 5 years ago
0
Use long reads as a binningsignal for hybrid assemblies only

#48 lauralwd closed 5 years ago
0
Should I use the non-hammer-corrected reads for binning and SNV detection?

#47 lauralwd closed 5 years ago
0
explicitly remove or compress output files in the assembly folders to slim down the project

#46 lauralwd opened 5 years ago
0
remove corrected reads after first assembly to slim down project

#45 lauralwd opened 5 years ago
0
remove binningsignal folders after succesfuly completing SNV detection in Anvio to slim down the project

#44 lauralwd opened 5 years ago
0
compress CAT tables by default

#43 lauralwd opened 5 years ago
0
Binning originalfiles

#42 lauralwd closed 5 years ago
0
introduce hybrid assemblies

#41 lauralwd closed 5 years ago
4
Less strict filtering with bowtie, should I re-run some assemblies.

#40 lauralwd closed 5 years ago
1
Combine CAT and BAT workflows to increase filtering quantity

#39 lauralwd closed 5 years ago
1
Subset filter

#38 lauralwd closed 5 years ago
0
samtools doesn't log propperly

#37 lauralwd closed 5 years ago
1
Binning originalfiles

#36 lauralwd closed 5 years ago
1
Binning originalfiles

#35 lauralwd closed 5 years ago
1
Subset filter

#34 lauralwd closed 5 years ago
1
split huge snakemake file in smaller files

#33 lauralwd opened 5 years ago
0
Binning originalfiles

#32 lauralwd closed 5 years ago
0
use chloroplast genome for filtering as well. Implement chloroplast download rule and a rule to merge it into the filterfasta file.

#31 lauralwd closed 5 years ago
1
Custom cat

#30 lauralwd closed 5 years ago
0
Custom cat

#29 lauralwd closed 5 years ago
0
Host orfs plant specific in a separate rule

#28 lauralwd closed 5 years ago
0
adapt CAT settings for better annotation

#27 lauralwd closed 5 years ago
6
implement plan B for assemblies that run out of memmory

#26 lauralwd closed 5 years ago
3
readme needs update

#25 lauralwd closed 5 years ago
0
R markdown document with assembly stats tables and figures

#24 lauralwd opened 5 years ago
0
merge snakemake shadow implementation of SPAdes assembly in development branch

#23 lauralwd closed 5 years ago
0
remove unnesecary output files once they are not needed anymore

#22 lauralwd closed 5 years ago
2
implement shadow directive in CAT rules

#21 lauralwd closed 5 years ago
0
Visualise binning sigals in an R markdown pdf per assembly

#20 lauralwd closed 5 years ago
1
Use both dedicated binning signals and sequencing reads used for assembly as input signals for binning

#19 lauralwd closed 5 years ago
1
Snakemake

#18 lauralwd closed 5 years ago
3
clarify and/or correct rule names.

#17 lauralwd opened 5 years ago
0
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 lauralwd closed 5 years ago
1
Binning

#15 lauralwd closed 5 years ago
0
update development branch to latest stable version

#14 lauralwd closed 5 years ago
0
Double filter

#13 lauralwd closed 5 years ago
0
reduce excessive output of SPAdes by implementing snakemake shadow rule

#12 lauralwd closed 5 years ago
0
allow for parallel prodigal processing in CAT classfication

#11 lauralwd closed 5 years ago
0
rule shorten scaffold_names: fix awk onliner

#10 lauralwd closed 5 years ago
0
testing commits of previously merched branches in double-filter branch

#9 lauralwd closed 5 years ago
0
Split spades strategy performs well and runs without errors.

#8 lauralwd closed 5 years ago
0
Merging final decission on bowtie settings into master

#7 lauralwd closed 5 years ago
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 lauralwd closed 5 years ago
0
Allow for failed SPAdes runs to keep (part) of the files and resume with more memory rather than starting over.

#5 lauralwd closed 5 years ago
2
make a mem_gb variable, automatically derived from the mem_mb variable

#4 lauralwd opened 5 years ago
0
get extra samples for binning signal

#3 lauralwd closed 5 years ago
1
acquire and organise all sequencing data from public repositories

#2 lauralwd closed 5 years ago
0
list and check and install all forseen dependencies

#1 lauralwd closed 5 years ago
0