From 196bbf849b6085250f33ed78c3cae15cd35606c0 Mon Sep 17 00:00:00 2001 From: GuilhemRoyer Date: Wed, 30 May 2018 17:55:35 +0200 Subject: [PATCH] Update README.md --- README.md | 34 ++++++++++++++++++++++++---------- 1 file changed, 24 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index ac3836f..eebbd00 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ However we think that this method can easily be applied to other bacterial speci You must install these dependencies before you start : -SPAdes 3.10.1 or later to run the assembly (header of contigs must be the same as in version 3.10.1) (http://bioinf.spbau.ru/spades) +SPAdes 3.10.1 or later if you want to run the assembly (= mode 1) (header of contigs must be the same as in version 3.10.1) (http://bioinf.spbau.ru/spades) Centrifuge 1.0.3 (https://github.com/infphilo/centrifuge) @@ -32,15 +32,29 @@ Centrifuge 1.0.3 (https://github.com/infphilo/centrifuge) usage: PlaScope.sh [OPTIONS] [ARGUMENTS] --h, --help display this message --t number of threads[OPTIONAL] [default : 8] --i fastq name (assumed to be filename_1.fastq.gz / filename_2.fastq.gz) [MANDATORY] ---fastq_dir path to fastq directory [MANDATORY] --o output directory [OPTIONAL] [default : current directory] ---db_dir path to centrifuge database [MANDATORY] ---db_name centrifuge database name [MANDATORY] - -Wrapper to launch PlaScope (SPAdes + Centrifuge-based plasmidic sequences classification) +General options: + -h, --help display this message + -t number of threads[OPTIONAL] [default : 8] + -o output directory [OPTIONAL] [default : current directory] + --sample Sample name [MANDATORY] + --db_dir path to centrifuge database [MANDATORY] + --db_name centrifuge database name [MANDATORY] + +Mode 1: SPAdes assembly + contig classification + -1 forward paired-end reads [MANDATORY] + -2 reverse paired-end reads [MANDATORY] + + +Mode 2: contig classification of a fasta file (only if you already have your SPAdes assembly!) + --fasta SPAdes assembly fasta file [MANDATORY] + + + +Example mode 1: +plaScope.sh -1 my_reads_1.fastq.gz -2 my_reads_2.fastq.gz -o output_directory --db_dir path/to/DB --db_name chromosome_plasmid_db --sample name_of_my_sample + +Example mode 2: +plaScope.sh --fasta my_fastafile.fasta -o output_directory --db_dir path/to/DB --db_name chromosome_plasmid_db --sample name_of_my_sample ```` ## *E. coli* database