A repository for some useful bio-scripts.
Summary Table
| Script | Type | System | Description | Note |
|---|---|---|---|---|
| L7_to_OTU | Bash |
Linux |
Summarzied OTU table -> OTU table | MacOS: gnu-opt required |
| ko2keggL.sh | Bash |
Linux |
update koID -> KEGG levels | MacOS: not tested |
| merge_bioms.R | R |
Unix/Win |
merge biom files by #OTU ID | MacOS: not tested |
| fq2fa.py | Python |
Unix/Win |
fastq -> fasta | MacOS/Win: not tested |
| extract_RGI_fasta.py | Python/Bio,pandas |
Unix/Win |
extract ORF using RGI output | MacOS/Win: not tested |
| q2-core.sh | QIIME 2 & q2meta-grouped.py |
Linux |
quick QIIME analysis with feature matrix | MacOS: gnu-opt required |
| q2-coreN.sh | QIIME 2 & q2meta-grouped.py |
Linux |
quick (non-phylogenetic) QIIME analysis with feature matrix | MacOS: gnu-opt required |
| q2meta-grouped.py | QIIME 2 |
Unix |
create grouped metadata for QIIME | MacOS: not tested |
| fq2dir.sh | Bash |
Uniux |
fastqs to sample-specific directory | Macos not tested |
| texlca.py | Python/pandas,argparse |
Unix/Win |
simple LCA taxonomy on text (LCS) | MacOS/Win: not tested |
| glines.py | Python/argparse |
Unix |
group ordered lines if meeting a substring | MacOS: not tested |