diff --git a/README.md b/README.md index 09e10d4..04d6f83 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,10 @@ -# NEWS 25.2. 2023 -The [preprint](https://www.biorxiv.org/content/10.1101/2023.02.24.529942v1) for Themisto v3 is out. A compiled executable file for Linux is available [here](https://github.com/algbio/themisto/releases/download/3.0.0/themisto_linux-v3.0.0.tar.gz). Tested to work at least on Ubuntu 18.04, Ubuntu 20.4, CentOS 7 and Red Hat 8.6. +# NEWS 13.4. 2023 + +Themisto version 3.1.0 is out. See the [release notes](https://github.com/algbio/themisto/releases/tag/3.1.0) for more information and pre-compiled Linux binaries. # About Themisto -Themisto is a succinct colored k-mer index supporting pseudo-alignment against a database of reference sequences similar to the tool Kallisto, Bifrost and Metagraph. For more information, see the [preprint](https://www.biorxiv.org/content/10.1101/2023.02.24.529942v1). +Themisto is a succinct colored k-mer index supporting pseudo-alignment against a database of reference sequences similar to the tool Kallisto, Bifrost and Metagraph. For more information, see the [preprint](https://www.biorxiv.org/content/10.1101/2023.02.24.529942v3). ## Requirements @@ -213,6 +214,15 @@ Usage: set intersection method. (default: 0.7) --include-unknown-kmers Include all k-mers in the pseudoalignment, even those which do not occur in the index. + --report-relevant-kmer-count + Appends to each output line a semicolon + followed by a space and then the number of + k-mers of the query that had at least 1 + color. + --relevant-kmers-fraction arg + Accept a pseudoalignment only if at least + this fraction of k-mers of the read had at + least 1 color. (default: 0.0) Computational resources options: -t, --n-threads arg Number of parallel execution threads. Default: 1