bustools

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nf-core / scrnaseq

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

workflow rna-seq pipeline nextflow single-cell kallisto 10x-genomics 10xgenomics nf-core bustools alevin cellranger star-solo

Updated Sep 11, 2026
Nextflow

pachterlab / kb_python

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A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

scrna-seq kallisto single-cell-rna-seq rna-velocity-estimation bustools kb-python

Updated Jun 9, 2026
Python

basilkhuder / Seurat-to-RNA-Velocity

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A guide to using a Seurat object in conjunction with RNA Velocity

kallisto seurat bustools anndata rna-velocity kb-python integrating-loom velocyto scvelo kallisto-bustools

Updated Dec 25, 2021

pachterlab / kallistobustools

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kallisto | bustools workflow for pre-processing single-cell RNA-seq data

rna-seq single-cell kallisto bustools

Updated Mar 10, 2026

Fazizzz / Low-Compute-SingleCell-QC-Nextflow-Pipeline

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Low-compute Nextflow pipeline for single-cell RNAseq QC using pseudo-alignment. Two-mode design: with laptop-friendly quick mode for QC and cost prediction, HPC/cloud full mode for Cell Ranger comparable results. Validated on Element AVITI and Illumina NextSeq 2000 sequencing data using 10X V3 Chromium chemistry. Outputs feed scanpy/Seurat directly

docker aws bioinformatics pipeline nextflow hpc scrna-seq single-cell kallisto qc ai-agents seurat fastp scanpy bustools

Updated May 22, 2026
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