Randomly subsample sequencing reads or alignments

Creating alignment plots from bam files

Identify which human reference genome was used to align a BAM/SAM/CRAM file

Identifies multiple SNVs within the same codon, reclassifies them as MNVs, and accurately computes resulting amino acid changes from genomic reads

Utility to check Binary Sequence Alignment / Map (BAM) files for corruption and repair them

Efficient gzip to BGZF transcoder using half-decompression (2-4x faster than decompress+recompress)

A lightweight wrapper to run minimap2 (v2.30) alignments directly on BAM file

Quick k-mer-based FASTA/FASTQ sequence record extraction, and SAM/BAM record filtering plus file annotation with k-mer tags.

High-performance SRA-to-SAM/BAM converter replacing NCBI sam-dump

AI algorithms visualization made with Rust

Filter BAM file based on read mean QV, implemented in Rust

an API for intersections of genomic data

Rust-powered BAM depth extraction with Python bindings

A drop-in replacement for UMI-tools, written in Rust. Same flags, same output - 14-91x faster.

High-performance BAM/SAM toolkit written in Rust 2024. Drop-in samtools-compatible CLI

extract nucleotide/read counts at user specific loci from multiple bam files

Pure-Rust BAM/VCF/BCF depth, pileup, variants & stats with Python bindings — native Linux/macOS/Windows wheels, pysam-parity, no htslib.

A colouriser for the SAM/BAM file format

A program that collapses CIGAR strings from SAM/BAM files making it short and easy to see which part of the read is clipped. Useful for long reads

Rust genomics toolkit for phased VCF/BCF MNVs, read evidence, BAM error models, and contamination probes