376 Open source projects that are alternatives of or similar to cljam

Frequently used commands in bioinformatics

Bioinformatics library in Kotlin

Syntax highlighting for computational biology

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

pythonic wrapper for htslib

My bioinfo toolbox

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

Fast and accurate sequence demultiplexing

Simple pure Python SAM parser and objects for working with SAM records

A Java API for high-throughput sequencing data (HTS) formats.

A D library for computational biology and bioinformatics

cython + htslib == fast VCF and BCF processing

annotate a VCF with other VCFs/BEDs/tabixed files

Sync paired-end FASTA/Q files and keep singleton reads

Home of the Genomic Feature and Variation Ontology (GFVO)

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

simple viewer for variant call format using htslib

A collection of scripts and notes related to genomics and bioinformatics

C library for high-throughput sequencing data formats

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

Python-based UCSC genome browser snapshot-taker and gallery-maker

Spark VCF data source implementation for Dataframes

Command line utility for manipulating Illumina-generated FastQ files.

find large indels (in the blind spot between GATK/freebayes and SV callers)

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Scalable genomic data analysis.

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Simple FASTQ quality assessment using Python

PERF is an Exhaustive Repeat Finder

Bayesian genotyper for structural variants

Haplotype VCF comparison tools

A curated list of bioinformatics bench-marking papers and resources.

Intuitive local web frontend for the BLAST bioinformatics tool

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Performant Pythonic GenomicRanges

A powerful open source data warehouse system

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Bayesian haplotype-based mutation calling

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

nim wrapper for htslib for parsing genomics data files

MISO: An open-source LIMS for NGS sequencing centres

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

GenomeTools genome analysis system.

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

A genome browser that shows long reads and complex variants better

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Code examples of fast and simple k-mer counters for tutorial purposes

🔬 BEDOPS: high-performance genomic feature operations

Chromosome visualization for the web

A tool to circularize genome assemblies

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

Deep learning infrastructure for bioinformatics

NGLess: NGS with less work

An R package for creating Q-Q and manhattan plots from GWAS results

JavaScript VisualizationTools

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

SDK for GPU accelerated genome assembly and analysis