sanger-pathogens/assembly-and-annotation-training sanger-pathogens/assembly-and-annotation-training

  • Stars
    star
    1
  • Language
    TeX
  • License
    Creative Commons ...
  • Created almost 4 years ago
  • Updated almost 4 years ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
sanger-pathogens/assembly-and-annotation-training
github

sanger-pathogens

Reviews

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

Repository Details

More Repositories

1

Roary

Rapid large-scale prokaryote pan genome analysis
Perl
317
star
2

circlator

A tool to circularize genome assemblies
Python
230
star
3

Artemis

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
Java
217
star
4

snp-sites

Finds SNP sites from a multi-FASTA alignment file
C
215
star
5

ariba

Antimicrobial Resistance Identification By Assembly
Python
167
star
6

assembly-stats

Get assembly statistics from FASTA and FASTQ files
C++
115
star
7

Fastaq

Python3 scripts to manipulate FASTA and FASTQ files
Python
70
star
8

pathogen-informatics-training

Jupyter Notebook
62
star
9

assembly_improvement

Improve the quality of a denovo assembly by scaffolding and gap filling
Perl
56
star
10

iva

de novo virus assembler of Illumina paired reads
Python
54
star
11

plasmidtron

Assembling the cause of phenotypes and genotypes from NGS data
Python
29
star
12

gff3toembl

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
Python
29
star
13

pymummer

Python3 module for running MUMmer and reading the output
Python
26
star
14

mlst_check

Multilocus sequence typing by blast using the schemes from PubMLST
Perl
24
star
15

saffrontree

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data
Python
24
star
16

Bio-Tradis

A set of tools to analyse the output from TraDIS analyses
Perl
22
star
17

companion

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion
Lua
21
star
18

seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads
Python
19
star
19

panito

Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment
C
16
star
20

nano-rave

Nextflow pipeline designed for rapid onsite QC and variant calling of Oxford Nanopore data (following basecalling and demultiplexing with Guppy).
Nextflow
10
star
21

Bio-RNASeq

The new Sanger Pathogen Informatics RNA Seq analysis pipeline
Perl
8
star
22

update_pipeline

Update a pipelines metadata
Perl
7
star
23

remove_blocks_from_aln

Python
5
star
24

Farmpy

Python3 package to handle job submission to a compute farm
Python
5
star
25

sanger-pathogens.github.io

Summary of Sanger Pathogen's Repos
Python
5
star
26

SnpEffWrapper

Takes a VCF and applies annotations from a GFF using SnpEff
Python
5
star
27

Bio-InterProScanWrapper

Perl
5
star
28

bact-gen-scripts

Python
4
star
29

Bio-ENA-DataSubmission

Perl
4
star
30

mapping-and-snp-calling-training

TeX
3
star
31

Bio-PacbioMethylation

Runs Pacbio methylation pipeline
Perl
3
star
32

unix-training

A set of jupyter notebooks to provide unix training developed by Pathogen Informatics at Wellcome Sanger Institute.
Jupyter Notebook
2
star
33

Bio-Metagenomics

Perl
2
star
34

setup_tracking

setup a vrtracking pipeline
Perl
2
star
35

pipelines_reporting

Perl
1
star
36

baker

A tool to generate configuration files and wrapper scripts
Python
1
star
37

chado-tools

Tools for accessing CHADO databases.
Python
1
star
38

Bio-ReferenceManager

Perl
1
star
39

Bio-AutomatedAnnotation

Perl module to take in an genomic assembly and produce annoation
Perl
1
star
40

fastml

Addtional functionality for fastml, see http://fastml.tau.ac.il
C++
1
star
41

iva-publication

Supplementary scripts and data for the IVA publication
Python
1
star
42

QC-training

Gnuplot
1
star
43

PathFind-training

Jupyter Notebook
1
star
44

Farm_blast

Python3 module to run blast+ or blastall in parallel on an LSF compute farm
Python
1
star
45

singularity-bsub

Provides wrapper scripts for executing LSF commands within a Singularity container
Shell
1
star
46

monocle

Python
1
star