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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