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correct reference to input from metagenomes to genomes #4

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correct reference to input from metagenomes to genomes #4

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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -41,7 +41,7 @@ The metadata file should be a tab delimited file. One of the columns should cont
## Usage:

The SynTracker pipeline is divided to two main steps:
a. Fragmentation of the reference genomes and execution of BLASTn search against the target genomes/metagenomes.
a. Fragmentation of the reference genomes and execution of BLASTn search against the target genomes (isolate genomes or MAGs).
b. Calculation of average pairwise synteny scores (APSS).
Each step is executed by a single command.

Expand Down Expand Up @@ -87,4 +87,4 @@ Changes to simplify and solve file naming procedure, and solve BLAST error resul
a. Added script "old_to_new_names.py": changes the file names in the target folder to "Sample.xxx", fasta headers to "contig.yyy", writes the changes to a table, and assigns all sequences to a single file. It is called from find_overlapping_regions.sh.
b. Modified "find_overlapping_regions.sh", to use "old_to_new_names.py" instead of sed command in step 1.
c. Modified "SynTracker.R" to read the table generated by "old_to_new_names.py" and change temporarily assigned sample names back to the original sample names (i.e., file names).
d. Changed "SynTracker_functions.R" to handle the new naming format.
d. Changed "SynTracker_functions.R" to handle the new naming format.