Home

Small Scripts for Small Bioinformatics Tasks

A collection of python scripts

1 Installation

conda create -n ssfsbt # (optional but recommended)
conda activate ssfsbt  # (optional but recommended)

git clone https://github.com/SimonHegele/SSfSBT
cd SSfSBT
pip install .

Will make scripts available as command-line-tools

2 Command-line-Tools

SSfSBT provides a variety of scripts available as command-line-tools.
Each is described in detail on the respective page of this wiki.

1. fa2fq
2. sample
3. lengths
4. kallisto2nanosim
5. busco_merge
6. unambiguous_codes
7. rnaQUASTcompare

3 File services

SSfSBT provides a variety of file services that can read from and write to various files used in bioinformatics. They are located in the file_services folder. Each file service is a class providing class methods.
Their read()-methods are generators, yielding dictionaries.
Their write()-methods accept iterables of dictionaries.

File type	Can read	Can write	Additional info
FASTA	✅	✅	Sequences
FASTQ	✅	✅	Sequences
PAF	✅	✅	Pairwise sequence alignments from Minimap2
SAM	✅	✅	Pairwise sequence alignments from basically any other alignment tool
BCALM (FASTA)	✅	❌	De Bruijn Graph from BCALM
FASTG (FASTA)	✅	❌	De Bruijn Graph from SPAdes