From 476f9b8004c392d2e7a149059b1d1a51850e505a Mon Sep 17 00:00:00 2001 From: Rauf Salamzade Date: Sat, 6 Jul 2024 15:15:01 -0500 Subject: [PATCH] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 6e39a10..d6d7ad0 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ [![Anaconda-Server Badge](https://anaconda.org/bioconda/skder/badges/platforms.svg)](https://anaconda.org/bioconda/skder) [![Anaconda-Server Badge](https://anaconda.org/bioconda/skder/badges/license.svg)](https://anaconda.org/bioconda/skder) -skDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics. +skDER (& CIDDER): efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics. > ***Note:*** Please make sure to use version 1.0.7 or greater to avoid a bug in previous versions! @@ -68,7 +68,7 @@ skDER features two distinct algorithms for dereplication (details can be found b #### CiDDER -In v1.2.0, we also introduced a second program called CiDDER (CD-hit based DEReplication) - which allows for optimizing selection of a minimal number of genomes that achieve some level of saturation of the pan-genome of the full set of genomes (see below for details). +In v1.2.0, we also introduced a second program called CiDDER (CD-hit based DEReplication) - which allows for optimizing selection of a minimal number of genomes that achieve some level of saturation of the pan-genome of the full set of genomes (see below for details). Note, CD-HIT determines protein clusters, not proper ortholog groups, and as such an approximation is made of the pan-genome space being sampled by representative genomes. ## Details on Dereplication Algorithms @@ -286,7 +286,7 @@ options: instead of performing a copy of the files. -c CPUS, --cpus CPUS Number of CPUs to use [Default is 1]. -m MEMORY, --memory MEMORY - The memory limit for CD-HIT in Gigabytes [Default is 4]. + The memory limit for CD-HIT in Gigabytes [Default is 0 = unlimited]. -u, --ncbi_nlm_url Try using the NCBI ftp address with '.nlm' for ncbi-genome-download if there are issues. ```