A collection of scripts intended for bacterial genomics (some might also be useful for eukaryotes ;-)).
- Summary
- Introduction
- Installation recommendations
- Dependencies
- UNIX loops
- Windows - UNIX linebreak problems
- License
(If a tool is not here yet it will be uploaded soon or write me a quick mail.)
- Basic stats for bases and reads in FASTQ files:
calc_fastq-stats - Concatenate multi-sequence (RichSeq or fasta) files to a single artificial file:
cat_seq - COG classification of proteins:
cdd2cog - Extraction of protein/nucleotide sequences from CDSs:
cds_extractor - MLST assignment and allele extraction for E. coli (Achtman scheme):
ecoli_mlst - Count all annotated primary features from RichSeq (e.g. embl or genbank) files:
get_genome_features - Batch downloading of sequences from NCBI's FTP server:
ncbi_ftp_downloadandncbi_e-utilities - Create an ortholog/paralog annotation comparison matrix from Proteinortho5 output:
po2anno - Protein search with blastp plus concise hit summary and optional alignment:
prot_finder - Regions of difference (ROD) detection:
rod_finder - NGS paired-end library insert size estimation from BAM/SAM:
sam_insert-size - And an assortment of smaller scripts for tasks like: sequence/alignment format converters (
seq_format-converter), dnadiff, GC% calculation etc.
Anyways you get the picture ...
All the scripts here are written in Perl (some include bash shell wrappers).
Each script is hosted in its own folder, so that a separate 'README.md' can be included for more information. However, all of the Perl scripts include additionally a usage/help text or a comprehensive POD (Plain Old Documentation) by calling the script either without arguments/options or option -h.
The scripts are only tested under UNIX, some won't run in a Windows environment (because of included UNIX commands). If you are on Windows an alternative might be Cygwin.
To download the repository, use either the 'Download zip' button on the right hand side or clone the repository with git:
git clone https://github.com/aleimba/bac-genomics-scripts.git
If there is an update to this GitHub repository (see above commits and releases), you can refresh your local repository by using the following command inside the local folder:
git pull
To install the scripts, copy them to your '/bin' folder and make them executable
$ chmod u+x script.pl
the scripts are then in your '$PATH' and can be run everywhere on your system. Of course you can just call them directly by prefexing 'perl' to the command or a './' for bash wrappers:
$ perl /path/to/script/script.pl <options>
or
$ ./script.sh <arguments>
Single scripts can be downloaded as well. For this purpose click on the folder you're interested in and then on the link of the script. There click on the Raw button and save this page to a file (without Raw you'll get an unusable html file). This is also true for other files (e.g. PDFs etc.).
Most of the Perl scripts include modules from BioPerl, which as a consequence has to be installed on your system. For BioPerl installation instructions see the website (How Do I...?...install BioPerl?).
Some scripts need additional Perl modules, which will be stated in the associated 'README.md' or POD. If they're not installed yet on your system get them from CPAN (installation instructions can be found on the website, see e.g. Getting Started or FAQ).
A very handy tip, if you want to run a script on all files in the current working directory you can use a loop in UNIX, e.g.:
$ for i in *.fasta; do perl script.pl -i $i; done
At last, some of the scripts don't like Windows formatted line breaks, you might consider running these input files through a nifty UNIX utility called dos2unix:
$ dos2unix input
All scripts are licensed under GPLv3 which is contained in the file LICENSE.
For help, suggestions, bugs etc. use the GitHub issues or write an email to aleimba [at] gmx [dot] de.