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.
Most are described in detail on the respective page of this wiki.

Tool	Summary
aln_pos2pos	Finding corresponding positions in multiple sequence alignments
busco_find	Extracting BUSCO transcript sequences
busco_merge	Merging multiple reports from BUSCO and compiling a plot
kallisto2nanosim	Converting expression profiles from Kallisto for NanoSim
lengths	Basic sequence length distribution analysis for one or more FASTA/FASTQ-files
lr_lordec_contam_filter	Filtering contamination from long reads corrected by HALC or LoRDEC with Kraken2 filtered short reads
fa2fq	FASTA to FASTQ conversion with different error rates for upper and lower case denoted nucleotides
fq2fa	FASTQ to FASTA conversion
gfa2fa	GFA to FASTA conversion
plot_msa	Plotting multiple sequence alignments
rnaQUASTcompare	Merging multiple reports from rnaQUAST and compiling a plot
sample	Subsampling a fixed number of sequences from FASTA/FASTQ-files
unambiguous_codes	Replacing ambiguity codes in FASTA/FASTQ-files

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