Results for samtool

SamTool is a Python library designed for easy integration of the SAM (Segment Anything with Masking) model into computer vision projects. SAM is a state-of-the-art model for segmenting objects in images with high accuracy.

the fast cli tool for samengine

Per-BED-region read depth — Rust port of samtools bedcov

Clip amplicon primer regions off aligned reads given a BED — Rust port of samtools ampliconclip

Group BAM reads by QNAME so mates are adjacent — Rust port of samtools collate

High-performance BAM/SAM/CRAM toolkit written in Rust 2024. Drop-in samtools-compatible CLI (view/sort/index/merge/markdup/flagstat) plus a library API for embedding directly into aligners and variant callers.

High-throughput, extensible SAM/BAM pileup generator

Amplicon sequencing statistics from primer BED + BAM — Rust port of samtools ampliconstats

Recompute the MD and NM aux tags against a reference FASTA — Rust port of samtools calmd

SAM/BAM/CRAM flag statistics — Rust port of samtools flagstat

Pure-Rust CLI over rust-htslib for BAM operations (view, sort, …). FFI-wrapper, output-compatible with samtools.

Per-position text pileup of read bases, qualities and map qualities — Rust port of samtools mpileup

Order-independent BAM checksum — Rust port of samtools checksum

Binder of samtools for ruby, on the top of FFI. This project was born from the need to add support of BAM files to the gee_fu genome browser (http://github.com/danmaclean/gee_fu).

Cagnut Samtools tools

Tabix file indexing routines from the samtools package http://samtools.sourceforge.net/

A minimal web service on the top of sinatra to query bam files

Iterate through a samtools pileup file

ools to work with fasta files, indexed with samtools. The initial releases depend on bio-samtools, but that will change

Bioruby core plugins

Wrapper of samtools for ruby. This project was born from the need to add support of BAM files to the gee_fu genome browser (http://github.com/danmaclean/gee_fu).