384 Open source projects that are alternatives of or similar to biowasm

An awk-like command-line tool for processing text, CSV, JSON, HTML, and XML.

Examples to get started with IBM Functional Genomics Platform

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

Large genome reassembly based on Hi-C data, continuation of GRAAL

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

Explore gnomAD datasets on the web

A secure encryption tool for genomic data

A library for manipulating bioinformatics sequencing formats in Apache Spark

CUT&RUN and CUT&Tag data processing and analysis

The GenePattern Server web application

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

jq zsh plugin

phenol: Phenotype ontology library

ntHash implementation in Rust

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

simple viewer for variant call format using htslib

A fast tool for hybrid genome assembly of long and short reads

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

SneakySnake🐍 is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.org/abs…

Manhattan plot Generator

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Improve the quality of a denovo assembly by scaffolding and gap filling

Introduction to the Command Line for Genomics

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

Finds SNP sites from a multi-FASTA alignment file

Collection of scripts for bacterial genomics

C development system for (Nitr)OS9/6x09, with source

Interactive jq (mirror)

Big Compute Learning Labs

It's my honor to drive you fucking fire faster, to have more time with your Family and Sunshine.This tool is for those who often want to search for a string Deeply into a directory in Recursive mode, but not with the great tools: grep, ack, ripgrep .........every thing should be Small, Thin, Fast, Lazy....without Think and Remember too much ...一…

Bead-based single-cell atac processing

A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

Bioconductor package for management of multi-assay data

Grep for something, then write the original files directly through the search results.

Multi-sample somatic variant caller

GA4GH Variation Representation Python Implementation

[unmantained] A playground for jq inside atom

Genome Interval Arithmetic in R

Ultrafast sequence typing and gene detection from NGS raw reads

Quickly check your project for typos

Transcripts annotation and GO enrichment Fisher tests

use the noise

Outline grep — search in indentation-structured texts (Rust version)

A jq playground, written in WebAssembly

SciFi theme for Conky

DriverPower

Analysing Capture Seq Count Data

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Nextflow basic tutorial for newbie users

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

a pileup library that embraces the huge

Forward-time simulation in Python using fwdpp

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

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

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

Explore rearrangements and copy-number amplifications in a cancer genome

Grep Web pages with extra features like JS deobfuscation and OCR