A collection of scripts intended for bacterial genomics (some might also be useful for eukaryotes) from high-throughput sequencing (aka next-generation sequencing).

• Summary
• Introduction
• Installation recommendations
• Dependencies
• UNIX loops
• Windows - UNIX linebreak problems
• Citation
• License
• Author - contact

• Basic stats for bases and reads in FASTQ files: calc_fastq-stats
• Concatenate multi-sequence files (RichSeq EMBL or GENBANK format, or FASTA format) to a single artificial file: cat_seq
• COG (cluster of orthologous groups) classification of proteins: cdd2cog
• Extraction of protein/nucleotide sequences from CDSs: cds_extractor
• MLST (multilocus sequence typing) assignment and allele extraction for Escherichia coli (Achtman scheme): ecoli_mlst
• Create a feature table for all annotated primary features in RichSeq (EMBL or GENBANK format) files: genomes_feature_table
• Deprecated! Batch downloading of sequences from NCBI's FTP server: ncbi_ftp_download
• Order sequence entries in FASTA/FASTQ files according to an ID list: order_fastx
• Create an ortholog/paralog annotation comparison matrix from Proteinortho5 output: po2anno
• Calculate stats and plot venn diagrams for genome groups according to orthologs/paralogs from Proteinortho5 output, i.e. overall presence/absence statistics for groups of genomes and not simply single genomes: po2group_stats
• Strain panel query protein search with BLASTP plus concise hit summary, optional alignment, and presence/absence matrix. Also included, scripts to transpose the matrix and calculate overall presence/absence statistics for groups of columns in the matrix: prot_finder
• Rename FASTA ID lines and optionally numerate them: rename_fasta_id
• Reverse complement (multi-)sequence files (RichSeq EMBL or GENBANK format, or FASTA format): revcom_seq
• Regions of difference (ROD) detection in genomes with BLASTN: rod_finder
• NGS paired-end library insert size estimation from BAM/SAM: sam_insert-size
• Randomly subsample FASTA, FASTQ, or TEXT files with reservoir sampling: sample_fastx-txt
• Convert a sequence file to another format with BioPerl: seq_format-converter
• Manual curation of annotation in NCBI's TBL format (e.g. from Prokka automatic annotation) in a spreadsheet software: tbl2tab
• Truncate sequence files (RichSeq EMBL or GENBANK format, or FASTA format) according to given coordinates: trunc_seq
• And an assortment of smaller scripts for tasks like (not yet uploaded to GitHub): alignment format converters, dnadiff, GC% calculation etc.

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|-help.

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' link after clicking the green 'Clone or download' button at the top 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 e.g. to a home /bin folder in your PATH and make them executable

$ find . \( -name '*.pl' -o -name '*.sh' -o -name '*.fas' -o -name '*.txt' \) -exec cp {} ~/bin \;
$ chmod u+x ~/bin/*.pl

the scripts can then 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.).

All scripts are tested with Perl v5.22.1.

Most of the Perl scripts include modules from BioPerl as stated in their respective README.md or POD, which as a consequence has to be installed on your system. For BioPerl installation instructions see the website (Installation).

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...Installing Perl Modules or FAQ).

Furthermore, some scripts call upon statistical computing language R and dependent packages for plotting purposes (again see the respective README.md or POD).

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 file in *.fasta; do perl script.pl "$file"; 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

For now cite the latest major release (tag: bovine_ecoli_mastitis) hosted on Zenodo:

Leimbach A. 2016. bac-genomics-scripts: Bovine E. coli mastitis comparative genomics edition. Zenodo. http://dx.doi.org/10.5281/zenodo.215824.

Also, all scripts have a version number (see option -v), which might be included in a materials and methods section.

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.

Andreas Leimbach (Microbial Genome Plasticity, Institute of Hygiene, University of Muenster)