18 projects
countmut
Unified ultra-fast strand-aware mutation counter (C backend + samtools-style -e/-p filters)
prismalign
N-color (2-color / 3-color / 3-nt) nucleotide-conversion alignment engine with pluggable backends
coralsnake
Exon-aware RNA pipeline: splicing-aware liftover (tbam2gbam/gbam2tbam), metagene, annotation
cutseq
Automatically cut adapter / barcode / UMI from NGS data
webblast
Fast NCBI BLAST searches via the interactive (website) queue — compact JSON results, adaptive polling and caching.
cfutils
Deprecated compatibility shim for the sanger package (renamed from cfutils)
sanger
Sanger sequencing toolkit
graph-easy
A Python port of Graph::Easy - lay out and render graphs as ASCII art
bwamem
Bindings to bwa aligner
markdup
Fast, accurate BAM deduplication with intelligent UMI detection and correct fragment detection
metagene
Metagene Profiling Analysis and Visualization
variant
annotate variant
omniclip
pipeclip
PIPELINE FOR CLIP SEQ DATA
scienv
One package for all scientific packages
treeio
A pure python parser for tree data format IO
molevo
Molecular Evoluition Simulator
fqutils
fastq file utils in python
