Update README.md

README.md

@@ -1,4 +1,4 @@
-### Release [v0.9.9](https://github.com/GenomicaMicrob/pair-end_cleaner/releases/latest)
+### Release [v1.0.1](https://github.com/GenomicaMicrob/pair-end_cleaner/releases/latest)
 
 # pair-end_cleaner
 Script to unzip, clean, assemble, and convert illumina pair-end fastq files in all subdirectories for 16S (V3, V4 and V3-V4 regions) and 18S (V9 region) amplicon data .
@@ -24,7 +24,7 @@ We have tested it extensively with files resulting of sequencing the V3 or V4 re
 4. Assembles both sequences.
 5. Converts from fastq to fasta.
 6. Renames the resulting sequences with the name of the sample only, it erases useless info, for example:
-  for files of a sample named sample01 (sample01_S01_L001_R1_001.fastq.gz, sample01_S01_L001_R2_001.fastq.gz) it will produce only sample01.
+  for files of a sample named *sample01* (sample01_S01_L001_R1_001.fastq.gz, sample01_S01_L001_R2_001.fastq.gz) it will produce only sample01.
 7. Renames all fasta header of a each file with the sample name and a consecutive number (>sample01_001, >sample01_002, etc.).
 8. Moves all resulting fasta files to a new folder named `assembled.current_date_time`, creates a report, a log file, and a csv file with the number of raw sequences processed, clean, assembled and low quality sequences per sample.
 
@@ -37,8 +37,8 @@ To assemble the pair-end sequences: [pear](https://sco.h-its.org/exelixis/web/so
 The best way to get pair-end_cleaner is to clone this repository directly to your linux:
 
 1. Download the latest [release](https://github.com/GenomicaMicrob/pair-end_cleaner/releases/latest).
-2. Make the script executable: `chmod +x pair-end_cleaner.v0.9.7.sh`.
-3. Copy pair-end_cleaner.sh to an appropiate directory in your linux system, `/usr/bin/` is a good choice to have it available for everyone: `sudo cp pair-end_cleaner.sh /usr/bin/`.
+2. Make the script executable: `chmod +x pair-end_cleaner.v1.0.1.sh`.
+3. Copy pair-end_cleaner.sh to an appropiate directory in your linux system, `/usr/bin/` is a good choice to have it available for everyone: `sudo cp pair-end_cleaner.v1.0.1sh /usr/bin/`.
 4. Log out and log in in order that execute it.
 
 ## Format of the sequence files
@@ -51,7 +51,7 @@ Usually, the Illumina sequencers produce the resulting files in the following fo
         sample02
            sample02_S02_L001_R1_001.fastq.gz
            sample02_S02_L001_R2_001.fastq.gz
-Sample results are nested in the main directory and in their corresponding subdirectory, they are compressed (.gz), and have a consecutive letter and number in the file name (_S01, _S02, etc.). Of course, since they are pair-end, we have two files per sample, one with the forward sequence (_R1) and the other with the reverse sequence (_R2).
+Sample results are nested in the main directory and in their corresponding subdirectory, they are compressed (.gz), and have a consecutive letter and number in the file name (_S01, _S02, etc.). Of course, since they are pair-end, we have two files per sample, one with the forward sequence (_L001_**R1**_001) and the other with the reverse sequence (_L001_**R2**_001).
 
 All this information is used by the script to process the files, so please do not change any of this, use it as they are downloaded from the sequencer, or from BASESPACE.
 
@@ -60,7 +60,7 @@ All this information is used by the script to process the files, so please do no
 ## Usage
 Go to the directory where you have all your subdirectories with the raw fastq files and type:
 
-`pair-end_cleaner.v0.9.9.sh`
+`pair-end_cleaner.v1.0.1.sh`
 
 It will present the following options:
 
@@ -78,13 +78,13 @@ It will present the following options:
         
 Just type the number for the region you have sequenced, or x to exit.
 
-For help, type `pair-end_cleaner.v0.9.9.sh -h`
+For help, type `pair-end_cleaner.v1.0.1.sh -h`
 
-For version and dependencies, `pair-end_cleaner.v0.9.9.sh -v`
+For version and dependencies, `pair-end_cleaner.v1.0.1.sh -v`
 
 ## Configuration
 
-For configuration details, `pair-end_cleaner.v0.9.9.sh -c`
+For configuration details, `pair-end_cleaner.v1.0.1.sh -c`
 
 To change the main configuration parameters (CPUs and Quality score) edit the script's code. Just change the values after the equal sign ( = ) in the 'configuration' section at the top of the script.