diff --git a/README.md b/README.md index f2d4ae5..d1422e2 100644 --- a/README.md +++ b/README.md @@ -116,6 +116,8 @@ After building the index, all but the refseq_abv.[1234].cfr index files may be r * #### Build custom database index The index building procedure is similar to [Centrifuge's](http://www.ccb.jhu.edu/software/centrifuge/manual.shtml#database-download-and-index-building), but with names changing to centrifuger. For example, centrifuge-download is centrifuger-download. +The folder "indices" contains information for creating index from other sources, like SILVA and GTDB. + * #### 10x Genomics data and barcode-based single-cell data If your input has barcode information, you can use "--barcode" to specify the barcode file and use "--read-format" to tell Centrifuger how to extract barcode information. The "--read-format" option can also specify the extraction for read1, read2 and UMI. The value for this argument is a comma-separated string, each field in the string is also a semi-comma-splitted string diff --git a/defs.h b/defs.h index 6f3578f..3f8f471 100644 --- a/defs.h +++ b/defs.h @@ -5,7 +5,7 @@ //#define DEBUG -#define CENTRIFUGER_VERSION "1.0.4-r152" +#define CENTRIFUGER_VERSION "1.0.4-r153" extern char nucToNum[26] ; extern char numToNuc[26] ; diff --git a/indices/README.md b/indices/README.md index f84b1f3..4eed7b8 100644 --- a/indices/README.md +++ b/indices/README.md @@ -16,3 +16,4 @@ The repetitiveness of GTDB representative genomes is very low, so the run-block ``` ../centrifuger-build -l gtdb_fname_to_taxid.map --taxonomy-tree gtdb_nodes.dmp --name-table gtdb_names.dmp -t 16 -o cfr_gtdb --build-mem 500G --offrate 5 --rbbwt-b 1 ``` +A pre-built index for GTDB r220 representative genomes is available at: https://www.dropbox.com/scl/fo/wtsermtdd62n1ttryuhwv/ADWTYiJA6Dh5gdbHmwC2nfo?rlkey=fgdpthjukcj1uhsjrcv35j927&dl=0 .