Projects in Awesome Lists tagged with bioinformatics-scripts

https://github.com/widdowquinn/find_differential_primers

Code for design of diagnostic PCR primers, and metabarcoding markers.

bioinformatics bioinformatics-scripts diagnostic-primers diagnostics primer-design qpcr

Last synced: 16 Mar 2025

https://github.com/bystrogenomics/bystro

Natural Language Search and Analysis of High Dimensional Genomic Data

bioinformatics bioinformatics-algorithms bioinformatics-analysis bioinformatics-databases bioinformatics-pipeline bioinformatics-scripts genomics genomics-search

Last synced: 17 Jan 2026

https://github.com/flystar233/pyscript-bio

生物信息学python代码，专注于重测序文本计算、处理

bioinformatics-scripts python3

Last synced: 26 Oct 2025

https://github.com/fomightez/sequencework

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

bioinformatics bioinformatics-analysis bioinformatics-scripts dna genomics list lists protein-sequences python rna

Last synced: 12 Apr 2025

https://github.com/dvklopfenstein/reactomepy

Explore biomolecular pathways in Reactome from the command-line or a Python script

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts bioinformatics-tool biological-networks biotech biotechnology molecular-biology pathway-analysis pathway-enrichment-analysis pathway-models protein-protein-interaction reactome reactome-pathway

Last synced: 19 Oct 2025

https://github.com/sydney-informatics-hub/bioinformatics

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts cancer genomics germline-variants indels metagenomics nextflow nextflow-pipelines ngs research-computing rnaseq snps somatic-variants sydney-informatics-hub transcriptomics variant-calling

Last synced: 11 Feb 2026

https://github.com/pwwang/biopipen

A set of processes/pipelines for bioinformatics

bioinformatics bioinformatics-pipeline bioinformatics-scripts pipeline-framework

Last synced: 13 May 2026

https://github.com/lazappi/binf-scripts

A collection of useful bioinformatics scripts.

bioinformatics bioinformatics-scripts

Last synced: 02 Aug 2025

https://github.com/peterk87/filter_classified_reads

Filter for reads from taxa of interest using Kraken2/Centrifuge classification results.

bioinformatics-scripts dna-sequences filtering taxonomic-classification

Last synced: 14 Jan 2026

https://github.com/fomightez/blast-binder

Repo for running command line-based BLAST in Jupyter environment provided via Binder.

bioinformatics bioinformatics-analysis bioinformatics-scripts dna genomics pandas pandas-dataframe protein-sequences python rna

Last synced: 14 Jul 2025

https://github.com/ulelab/peka

Find motifs enriched around prominent crosslinks

bioinformatics bioinformatics-analysis bioinformatics-scripts

Last synced: 17 Jan 2026

https://github.com/fomightez/pdbepisa-binder

Using data from PDBePISA with the convenience of Python and Jupyter.

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts genomics nucleic-acids nucleic-sequence pandas pandas-dataframe protein-sequences protein-structure python snakemake

Last synced: 31 Aug 2025

https://github.com/orangesi/pykits

simple python script for bioinformatics

bioinformatics-scripts biopython fasta fire-python pandas-python python3

Last synced: 28 Feb 2025

https://github.com/pritampanda15/youtube-tutorials

Tutorials on bioinformatics, computational biology, molecular dynamics, and other specialized scientific tools and workflows.

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts tutorials youtube

Last synced: 22 Oct 2025

https://github.com/fomightez/pdbsum-binder

Demonstrating analysis of PDBsum-related data via active Jupyter sessions provided via MyBinder.org

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts genomics pandas pandas-dataframes protein-sequences protein-structure python snakemake

Last synced: 30 Jan 2026

https://github.com/seb943/smith_waterman_py

Implementing the Smith-Waterman algorithm in Python

bioinformatics bioinformatics-scripts bioinformatics-tool dynamic-programming python smith-waterman smith-waterman-algorithm

Last synced: 15 Jun 2025

https://github.com/conorheffron/global-max-sim-matrix

Compute Global Maximum Similarity Matrix for 2 Sequences

bioinformatics-analysis bioinformatics-scripts global-max-similarity-matrix matrices needleman-wunsch-alignment r

Last synced: 12 Sep 2025

https://github.com/mbhall88/tinysink

Synchronise Nanopore reads with a server.

bioinformatics-scripts fast5 oxford-nanopore

Last synced: 18 Mar 2025

https://github.com/dogth/biomultitool

GUI for a few tools

bioinformatics bioinformatics-scripts

Last synced: 24 Mar 2025

https://github.com/mikeph52/biogenie

BioGenie is a complete bioinformatics command line tool, written in C++.

bioinformatics bioinformatics-pipeline bioinformatics-scripts bioinformatics-software bioinformatics-tool dna dna-sequences pipeline protein rna-seq

Last synced: 06 Mar 2026

https://github.com/chrisarg/alien-seqalignment-last

Sequence Alignment tool

bioinformatics bioinformatics-analysis bioinformatics-scripts sequence sequence-alignment

Last synced: 26 Mar 2025

https://github.com/chrisarg/alien-seqalignment-edlib

Sequence Alignment tool

bioinformatics bioinformatics-analysis bioinformatics-scripts sequence-alignment sequencing

Last synced: 26 Mar 2025

https://github.com/chrisarg/alien-seqalignment-mmseqs2

Sequence Alignment tool

bioinformatics bioinformatics-analysis bioinformatics-scripts sequence-alignment sequencing

Last synced: 26 Mar 2025

https://github.com/chrisarg/alien-seqalignment-minimap2

Sequence Alignment tool

bioinformatics bioinformatics-analysis bioinformatics-scripts bioinformatics-tool sequence-alignment sequencing

Last synced: 26 Mar 2025

https://github.com/ulelab/bs_assign

Find groups of motifs around genomic landmarks of interest

bioinformatics bioinformatics-analysis bioinformatics-scripts

Last synced: 17 Jan 2026

https://github.com/matthew-mosior/humo-create-variant-file

A Haskell script that creates a master variant file given sample information and variant information.

bioinformatics-scripts haskell tsv

Last synced: 13 Oct 2025

https://github.com/matteodelucchi/tr_cnv_in_expression_data

Pipeline to prepare RNA sequencing data for tandem repeat annotation with TRAL

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts bioinformatics-tool cloud-computing

Last synced: 24 Apr 2026

https://github.com/ibchgenomic/genome-estimates

estimates genomes size using the flow cytometry

bioinformatics bioinformatics-scripts flowcytometry genome genome-analysis genome-informatics

Last synced: 30 Mar 2025

https://github.com/chrisarg/alien-seqalignment-bowtie2

Sequence Alignment tool

bioinformatics bioinformatics-analysis bioinformatics-scripts sequence-alignment sequencing

Last synced: 26 Mar 2025

https://github.com/umbertodellamonica/fp-mash

Fp-Mash contains an adaptation of the Mash tool specifically designed to process fingerprints as part of the lyn2vec project. The main objective is to leverage the capabilities of Mash for fast and efficient genome and metagenome distance estimation, and apply these features to the vectorization tasks in lyn2vec

bio bioinformatics bioinformatics-analysis bioinformatics-scripts bioinformatics-tool

Last synced: 22 Feb 2025

https://github.com/adeschen/mpileuptools

This python script parses a mpileup file to extract the coverage of each base at each position.

bioinformatics bioinformatics-scripts coverage mpileup parser position python27

Last synced: 18 Mar 2025

https://github.com/ibchgenomic/bacterial-ko-phylogenomics

analyzing bacterial genome based ontologies and phylogenomics informativeness

bioinformatics bioinformatics-scripts genome-analysis genome-annotation metagenomics metagenomics-analysis metagenomics-bioinformatics metagenomics-data phylogenomics phylogenomics-pipeline

Last synced: 18 Mar 2025

https://github.com/sciencegenome/genome-estimates

estimates genomes size using the flow cytometry

bioinformatics bioinformatics-scripts flowcytometry genome genome-analysis genome-informatics

Last synced: 11 Jun 2025

https://github.com/matthew-mosior/basic-variant-selector

A Haskell script for selecting variants from a variant calling format (vcf) file based on variants present in a mgibed file.

bioinformatics-scripts haskell manual-review somatic-variants variant-call-format

Last synced: 23 Jun 2025

https://github.com/matthew-mosior/variant-to-bam-readcount

A Haskell script for creating input files for bam-readcount from ensembl-vep output and variant-calling format (vcf) files.

bam-readcount bioinformatics-scripts haskell somatic-variants

Last synced: 23 Jun 2025

https://github.com/matthew-mosior/fasta-region-randomizer

A Haskell script for creating random single nucleotide variants within genomic region(s) using a genomic window string.

bioinformatics-scripts genomics pseudo-random-generator random-snv

Last synced: 23 Jun 2025

https://github.com/matthew-mosior/representative-sample-chooser

A Haskell script that performs hierarchical filtering on a tab-delimited file across groups of lines based on user-defined hierarchical filtering string.

bioinformatics-scripts haskell hierarchical-data-filter text-filter

Last synced: 23 Jun 2025