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agat

Another Gtf/Gff Analysis Toolkit

bam-analysis-kit

bbmeth

BBMeth: An R package for fitting methylation data with a beta-binomial model

bc

Template for Software Carpentry bootcamp site repository.

bioawk

BWK awk modified for biological data

bioinformatics-training

Bioinformatics training resources

brahmanangusassemblyscripts

brb-seqtools

Suite of tools for processing BRB-seq data

canu

A single molecule sequence assembler for genomes large and small.

cgmaptools

toolbox for analysing BS-seq data, advance features in SNV, ASM and DMR

cheat

cheat allows you to create and view interactive cheatsheets on the command-line. It was designed to help remind *nix system administrators of options for commands that they use frequently, but not frequently enough to remember.

circast

CircAST is a computational tool for circular RNA full-length assembly and quantification using RNA-Seq data.

dart

DART – a fast and accurate RNA-seq mapper with a divide-and-conquer strategy

datasciencespecialization.github.io

http://DataScienceSpecialization.github.io

dge_workshop_salmon_online

docker4seq

Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers.

dragmap

DRAGEN open-source mapper

e-bike-edge-multifield

easyamplicon

Easy Amplicon data analysis pipeline

edda

Source for course materials at http://ged.msu.edu/angus/

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

ena-fast-download

Download FASTQ files of reads from the European Nucleotide Archive (ENA)

enigma2_pre_start

esp-idf

Espressif IoT Development Framework. Official development framework for Espressif SoCs.

estimate_genome_size.pl

Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish

falcon

FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries

falcon-phase

FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds

faqcs

Quality Control of Next Generation Sequencing Data

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

fishpond

Differential transcript and gene expression, as well as helper functions for working with Salmon, alevin, and alevin-fry data