Start from 2023-02-28
For access to 'jiang@azur' at the first time, please contact Jiang[^2].
It is possible to refer to all the usages listed here on your own terminal if you have a similar environment and OS. Free to ask if have any questions.
[^1]: All Rights Reserved. [^2]: You should know where to find him^.^
ALWAYS enter your directory first cd user_name before any action!
DO NOT install, update or modify anything without contact!
CONTACT first if you want new packages or environments!
| 00 | base | 2023-02-28 | basic environment, common usages | |
| 01 | anvio-7.1 | 2023-02-28 | anvi'o for pangenome / metagenome analyses | |
| 02 | assembly | 2023-02-28 | tools for genome assembly: seqkit, fastqc, unicycler, flye, medaka, pilon ... | |
| 03 | gtdbtk-2.1.1 | 2023-02-28 | env 12 | gtdbtk tool for GDTB |
| 04 | checkm | 2023-02-28 | env 13 | genome quialty check (checkm or gunc), completeness and contamination |
| 05 | pydata | 2023-02-28 | data analysis using python | |
| 06 | r-env | 2023-02-28 | data analysis using R | |
| 07 | unicycler050 | 2023-02-13 | only unicycler 0.5.0 | |
| 08 | qiime2-2023.2 | 2023-03-10 | env 14 | for qiime2 analyses |
| 09 | ncbi | 2023-03-28 | 2023-07-12 | local blast using blast+ or diamond |
| 10 | prokka | 2023-07-03 | rapid prokaryotic genome annotation | |
| 11 | rna-seq | 2023-11-02 | RNA seq analysis: Trimmomatic, Trinity | |
| 12 | gtdbtk-2.4.0 | 2024-05-14 | gtdbtk-2.4.0 with new GTDB-Tk reference dataset R220 (ver202404) | |
| 13 | checkm2 | 2024-06-04 | MAGs quality check: checkM2, QUAST, GUNC | |
| 14 | qiime2-amplicon-2024.5 | 2024-06-05 | The 2024.5 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 framework, q2cli and the following plugins: q2-alignment, q2-composition, q2-cutadapt, q2-dada2, ... | |
| 15 | qiime2-metagenome-2024.5 | 2024-06-07 | The 2024.5 release of the QIIME 2 Metagenome Distribution includes the QIIME 2 framework, q2cli (a QIIME 2 command-line interface) and the following plugins: q2-assembly, q2-composition, q2-cutadapt, q2-demux, ... | |
| 16 | metawrap | 2024-06-10 | MetaWRAP environment, a flexible pipeline for genome-resolved metagenomic data analysis: metawrap-mg, blast, concoct, maxbin2, megahit, metabat2, … Databases installed: checkm, ncbi_nt, ncbi_tax, SILVA 16S | |
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Basic information on this space and the general list of environments please check here.
Detailed list of environments and packages please check here.
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