From 2aa22678ca29ce59bdda512945094e817c633437 Mon Sep 17 00:00:00 2001 From: Lucas Sinclair <649288+xapple@users.noreply.github.com> Date: Wed, 1 May 2024 15:11:28 +0200 Subject: [PATCH] Rename the old "silvamod138" to "silvamod138pr2" everywhere --- README.md | 12 ++++++++---- docs/install_from_source.md | 2 +- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index e965986..2810e25 100644 --- a/README.md +++ b/README.md @@ -42,6 +42,10 @@ Since `crest4` is written in python it is compatible with all operating systems: $ conda install -c bioconda -c conda-forge -c xapple crest4 +Or to create a custom environment named `crest` which you activate later: + + $ conda create -n crest -c bioconda -c conda-forge -c xapple crest4 + ### Installing via `pip` $ pip3 install crest4 @@ -96,7 +100,7 @@ To parallelize the sequence similarity search with 32 threads use this option: crest4 -f sequences.fasta -t 32 -Silvamod138 is the default reference database. To use another database, e.g., midori, the `-d` option must be specified followed by the database name: +Silvamod138pr2 is the default reference database. To use another database, e.g., midori, the `-d` option must be specified followed by the database name: crest4 -f sequences.fasta -d midori248 @@ -223,19 +227,19 @@ In such a case you just need to copy the hits file that was generated back to yo To create the hits file on a different server you should call the `blastn` executable with the following options: - blastn -query sequences.fasta -db ~/.crest4/silvamod138/silvamod138.fasta -num_alignments 100 -outfmt "7 qseqid sseqid bitscore length nident" -out seq_search.hits + blastn -query sequences.fasta -db ~/.crest4/silvamod138pr2/silvamod138pr2.fasta -num_alignments 100 -outfmt "7 qseqid sseqid bitscore length nident" -out seq_search.hits We also recommend that you use `-num_threads` to enable multi-threading and speed up the alignments. The equivalent VSEARCH command is the following: - vsearch --usearch_global sequences.fasta -db ~/.crest4/silvamod138/silvamod138.udb -blast6out seq_search.hits -threads 32 -id 0.75 -maxaccepts 100 + vsearch --usearch_global sequences.fasta -db ~/.crest4/silvamod138pr2/silvamod138pr2.udb -blast6out seq_search.hits -threads 32 -id 0.75 -maxaccepts 100 ## More information ### Classification databases -The `silvamod138` database was derived by manual curation of the [SILVA NR SSU Ref v.138](https://www.arb-silva.de) for Bacteria, Archaea, Metazoa and Fungi. For other eukaryotes (protists), the [PR2 v4.13 database](https://pr2-database.org/) was used. The SILVA database used was last release in August 2020 and PR2 database in March 2021. +The `silvamod138pr2` database was derived by manual curation of the [SILVA NR SSU Ref v.138](https://www.arb-silva.de) for Bacteria, Archaea, Metazoa and Fungi. For other eukaryotes (protists), the [PR2 v4.13 database](https://pr2-database.org/) was used. The SILVA database used was last release in August 2020 and PR2 database in March 2021. The `silvamod128` database was derived by manual curation of the [SILVA NR SSU Ref v.128](https://www.arb-silva.de/documentation/release-128/). It supports SSU sequences from bacteria and archaea (16S) as well as eukaryotes (18S), with a high level of manual curation and defined environmental clades. This database was last released in September 2016. diff --git a/docs/install_from_source.md b/docs/install_from_source.md index 1f8852b..f083d2e 100644 --- a/docs/install_from_source.md +++ b/docs/install_from_source.md @@ -86,6 +86,6 @@ Since `crest4` is now installed from source, there is no executable on the `$PAT Instead, to launch `crest4` from the command line, one must proceed as so and add a `python3 -m` suffix to each command: - $ python3 -m crest4 -f ~/test/sequences.fasta -d silvamod138 -t 4 + $ python3 -m crest4 -f ~/test/sequences.fasta -d silvamod138pr2 -t 4 You do not need to run the `setup.py` script at any moment. \ No newline at end of file