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abi2fastq

abi2fastq is a small utility to convert Sanger sequencing reads in .abi (applied biosystems) format to FASTQ

adegenet

adegenet: a R package for the multivariate analysis of genetic markers

agrep

AGREP - approximate GREP for fast fuzzy string searching. Files are searched for a string or regular expression, with approximate matching capabilities and user-definable records. Developed 1989-1991 by Udi Manber, Sun Wu et al. at the University of Arizona. ISC open source license since Sept. 2014.

agriplex_targeted_dnaseq

Validation of nonsynonymous snv and indel calls in Gallus gallus Marek's disease lymphomas

alignment-and-variant-calling-tutorial

basic walk-throughs for alignment and variant calling from NGS sequencing data

alignments

filtering phix 1st

alignqc

Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysis results.

aptamerbase

Aptamers are single-stranded nucleic acid or amino acid polymers that recognize and bind to targets with high affinity and selectivity. The Aptamer Base is a database of detailed, structured information about the experimental conditions under which aptamers were selected and their binding affinity quantified.

aptasuite

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.

awesome

😎 Awesome lists about all kinds of interesting topics

bam-readcount

count DNA sequence reads in BAM files

basecalling-comparison

A comparison of different Oxford Nanopore basecallers

basset

Convolutional neural network analysis for predicting DNA sequence activity.

bb

Bioinformatics utilities

bedtools2

A powerful toolset for genome arithmetic.

bigscale

An Analytical Framework for Big-Scale Single Cell Data

c-kmeroligo

cadnano2.5

PyQt5 version of cadnano

centrifuge

Classifier for metagenomic sequences

chromosomer

A reference-assisted assembly tool for producing draft chromosome sequences.

city-roads

Visualization of all roads within any city

clustringr

R package for clustering strings by edit distance using graph algorithms (connected components and edge-betweeness)

crispresso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

crispresso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

crossmap

CrossMap is a python program to lift over genome coordinates from one genome version to another.

crossmap-workflow

Workflow and script for converting genomic coordinates using MUMmer output and CrossMap

damage-estimator

Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such as transposon based methods and Ultra II FS library preparation from NEB).

dascrubber-wrapper

Wrapper script for easier read scrubbing with DASCRUBBER

data-science-cheatsheet

A helpful 4-page data science cheatsheet to assist with exam reviews, interview prep, and anything in-between.

deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine