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arumugamlab
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MIntO
Pipeline for Reproducible and Scalable Integration of Metagenomic and Metatranscriptomic Data
MIT License
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Cleanup of bwa index mirrors and automatic estimation of vamb memory usage
#75
microbiomix
closed
4 days ago
0
Speed-ups, additional input method, change in batches for binning and added raw read QC
#74
jszarvas
closed
2 weeks ago
2
Removed 'this.path' and 'include' dependencies
#73
arumugamlab
closed
1 month ago
0
Avoiding too many zcats and gzips
#72
microbiomix
closed
1 month ago
0
Saving space during binning - by gzipping files and ignoring useless columns
#71
microbiomix
closed
1 month ago
0
Replaced 'bedtools multicov' with 10X faster 'samtools bedcov'
#70
microbiomix
closed
1 month ago
1
BWA index files are made as regular shadow rule and rsync'ed to nodes
#69
microbiomix
closed
1 month ago
0
Using checkpoints to create assembly batches for depth calculation
#68
microbiomix
closed
1 month ago
0
Parallelized the bottleneck step of 'bedtools multicov'
#67
microbiomix
closed
1 month ago
0
Moved taxonomical annotation versions into gene_annotation
#66
jszarvas
closed
1 month ago
0
Cluster-friendly implementation of bwa index to automatically distribute files to nodes
#65
microbiomix
closed
1 month ago
1
Updated example yaml files; Improved search for runs per sample.
#64
microbiomix
closed
2 months ago
0
Fixed issues with 'MERGE_ILLUMINA_SAMPLES' directive; and other minor improvements
#63
microbiomix
closed
2 months ago
0
BUGFIX: Gene/function abundance/expression plots mislabels
#62
microbiomix
closed
2 months ago
0
Gene annotation in batches; Made it easier to skip QC and start MIntO with assembly or mapping to refgenome
#61
microbiomix
closed
2 months ago
0
Bugfix: eggnog db version
#60
jszarvas
closed
2 months ago
0
Make host-removal and other QC steps optional
#59
CJREID
closed
2 months ago
3
Handle unassigned/unclassified taxa in metaphlan and motus
#58
microbiomix
closed
2 months ago
0
Update gene_annotation.smk
#57
CJREID
closed
2 months ago
1
Upgraded test script to use v2.2.0 when released
#56
microbiomix
closed
3 months ago
0
Taxonomic profiles from read-mapping in MAG/refgenome modes; other bug -fixes and improvements
#55
microbiomix
closed
3 months ago
2
Optional COAS_factor, more flexible sample names and tax. profile plotting
#54
jszarvas
closed
3 months ago
0
Bugfix number of lines in concatting individual annotation files
#53
jszarvas
closed
3 months ago
0
Feature request: custom DB locations
#52
CJREID
opened
3 months ago
0
Safely handling sample names as strings; Other bug fixes
#51
microbiomix
closed
4 months ago
0
Reordered rules and added comments for easier comprehension
#50
microbiomix
closed
4 months ago
0
Removed redundant rules; Moved marker gene identification from gene_abundance to gene_annotation.
#49
microbiomix
closed
4 months ago
0
Removed unnecessary config variables from yaml files
#48
microbiomix
closed
4 months ago
0
Added shadow directive to gtdb download
#47
jszarvas
closed
4 months ago
0
Upgraded metaphlan, phylophlan and GTDB versions/databases. Other minor improvements
#46
microbiomix
closed
4 months ago
0
Feature: bulk input in one folder
#45
jszarvas
closed
4 months ago
0
TSVs only for tabular output; BED coordinate bugfix; more file compression
#44
microbiomix
closed
4 months ago
0
Bugfix motus version print after moving the db
#43
jszarvas
closed
4 months ago
0
Streamlining/simplifying directory structure, using GNU parallel within rules for further speedup, smaller output file footprints
#42
microbiomix
closed
4 months ago
0
Software and database versions
#41
jszarvas
closed
4 months ago
0
Efficient reimplementation of generating & merging single-sample profile files to save disk space, memory and time. Plus other efficiency improvements.
#40
microbiomix
closed
5 months ago
0
Removed unnecessary 'mag_omics' from 'data_integration.yaml'
#39
microbiomix
closed
5 months ago
0
Gene/functional profiling - Saving disk space and runtime by further optimization
#38
microbiomix
closed
5 months ago
0
Several improvements in annotation and profiling - outputs remain unchanged
#37
microbiomix
closed
5 months ago
0
Bringing back lost kofamscan runtime fix (d1fe76a)
#36
microbiomix
closed
5 months ago
0
Bringing back explicit arguments to annotation collation script
#35
microbiomix
closed
5 months ago
0
Update collate script and bugfixes
#34
jszarvas
closed
5 months ago
0
Minor improvements
#33
microbiomix
closed
5 months ago
0
Renamed functional categories to be more structured and logical
#32
microbiomix
closed
5 months ago
2
Function profiling enabled for large number of MAGs
#31
microbiomix
closed
5 months ago
0
New minor features; updated yaml file examples; bug fixes
#30
microbiomix
closed
6 months ago
0
Bugfixes and speed-ups for gene_annotation and mags_generation
#29
jszarvas
closed
6 months ago
0
Function profiling enabled for large number of MAGs
#28
microbiomix
closed
6 months ago
0
MAG taxonomy bug
#27
microbiomix
closed
7 months ago
0
Update to dbCAN 4.1 and switch to individual processing of MAGs
#26
jszarvas
closed
6 months ago
0
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