harvardinformatics/AnnotationBRAKER harvardinformatics/AnnotationBRAKER

  • Stars
    star
    2
  • Language
    Python
  • Created 5 months ago
  • Updated 4 months ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
harvardinformatics/AnnotationBRAKER
github

harvardinformatics

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

Workflows and code for generating and filtering genome annotations with BRAKER

More Repositories

1

learning-bioinformatics-at-home

resources for learning bioinformatics
805
star
2

JAuth

Java GUI client to generate Google authentication codes
Java
196
star
3

bioinformatics-coffee-hour

Short lessons from FAS Informatics coffee hour
HTML
141
star
4

ATAC-seq

Python
119
star
5

snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
Python
69
star
6

GenomeAnnotation

Best practices and workflow for genome annotation
Python
66
star
7

TranscriptomeAssemblyTools

A collection of scripts for processing fastq files in ways to improve de novo transcriptome assemblies, and for evaluating those assemblies.
Python
47
star
8

degenotate

Python
41
star
9

micro-course

Code for Informatics nano course
HTML
11
star
10

spunnel

Spank Tunnels
Groff
9
star
11

TranscriptomeAssemblyEvaluation

Workflows and scripts used to perform analyses for de novo transcriptome assembly manuscript
Python
9
star
12

AnnotationTOGA

Guidelines for running TOGA and scripts for processing outputs
Python
6
star
13

scrub-jay-genomics

HTML
4
star
14

website

Website markdown files
HTML
4
star
15

PandAnnotate

A python-based alternative to Trinotate for merging herterogeneous transcriptome assembly annotation tables
Python
3
star
16

specify_web

Conversion of HUH specify_web application to git
PHP
3
star
17

infoscripts

C
3
star
18

ifxdjango

Django project template for ifx Django REST / VueJS / Vuetify applications
Python
3
star
19

GenomeAnnotation-WholeGenomeAlignment

guidelines for running progressive CACTUS to produce a whole genome alignment required for genome annotation tools that leverage WGA
Python
3
star
20

GenomeAnnotation-Maker

Guidelines for running MAKER
2
star
21

nanopore-assembly

2
star
22

imagej_processing

Demo files for ImageJ (headless) macro processing and SLURM scripts for Office Hours/Tips at 12
Shell
2
star
23

econ

Economic botany application
Ruby
2
star
24

python-workshop

Python workshop materials
Python
2
star
25

iggybase

iggybase is a general database frontend. First, we are rolling it out as Laboratory Information Management System (LIMS).
HTML
2
star
26

bulk_RNA-seq

Best practices, scripts and workflows for performing bulk RNA-seq expression analyses
Python
2
star
27

pacbio_hifi_assembly

A snakemake workflow for assembly with HiFi
Python
2
star
28

GenomeAnnotation-ComparativeAugustus

Guidelines for running multi-genome AUGUSTUS, and scripts for processing outputs
2
star
29

rcsqueue

Python
2
star
30

bioblog

Useful bioinformatics scripts
Perl
2
star
31

BulkRNAseq2Counts

A Snakemake workflow for generating expression count tables from either locally stored fastq files or NCBI-SRA accessions for bulk RNA-seq
Python
2
star
32

ratites

Code for Scott Edwards ratite grant.
1
star
33

specify_rapid

Rapid data upload tool for specify. Conversion from SVN.
JavaScript
1
star
34

minilimsdb

The database component for MiniLIMS. Used for containerization.
1
star
35

GenomeAnnotation-Braker

Guidelines for running BRAKER, and scripts for processing outputs
Python
1
star
36

hex

Shell command API
Python
1
star
37

specify-huh

git version of the HUH specify svn repo
Java
1
star
38

PhyloAcc-interface

Front-end for PhyloAcc
Python
1
star
39

intro-to-bwa

Informatics Coffee Hour demo
Jupyter Notebook
1
star
40

quantproteomics

Python
1
star
41

harvard_doc

Standalone application for creating Harvard-branded PDFs
Python
1
star
42

AnnotationRNAseqAssembly

Snakemake workflow for assembling transcript models from RNA-seq reads
Python
1
star