tseemann/skrofula tseemann/skrofula

  • Stars
    star
    5
  • Rank 2,861,937 (Top 57 %)
  • Language
    Perl
  • License
    GNU General Publi...
  • Created about 5 years ago
  • Updated over 4 years ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
tseemann/skrofula
github

tseemann

Reviews

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

Repository Details

Yet another M.tuberculosis typing and resistance tool, but for the impatient (not in-patient)

More Repositories

1

prokka

โšก โ™’ Rapid prokaryotic genome annotation
Perl
808
star
2

snippy

โœ‚๏ธ โšก Rapid haploid variant calling and core genome alignment
Perl
471
star
3

abricate

๐Ÿ”Ž ๐Ÿ’Š Mass screening of contigs for antimicrobial and virulence genes
Perl
359
star
4

shovill

โšกโ™ ๏ธ Assemble bacterial isolate genomes from Illumina paired-end reads
Perl
210
star
5

barrnap

๐Ÿ”ฌ โ™Œ Bacterial ribosomal RNA predictor
Perl
200
star
6

mlst

๐Ÿ†” Scan contig files against PubMLST typing schemes
Shell
191
star
7

nullarbor

๐Ÿ’พ ๐Ÿ“ƒ "Reads to report" for public health and clinical microbiology
Perl
134
star
8

snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment
C
126
star
9

any2fasta

Convert various sequence formats to FASTA
Perl
115
star
10

VelvetOptimiser

๐Ÿ“ˆ Automatically optimise three of Velvet's assembly parameters.
Perl
47
star
11

samclip

Filter SAM file for soft and hard clipped alignments
Perl
44
star
12

phastaf

Identify phage regions in bacterial genomes for masking purposes
Perl
29
star
13

seeka

Get microbial sequence data easier and faster
Perl
28
star
14

homebrew-bioinformatics-linux

๐Ÿบ ๐Ÿง Homebrew formulae for bioinformatics software only available for Linux
Ruby
27
star
15

berokka

๐ŸŠ ๐Ÿ’ซ Trim, circularise and orient long read bacterial genome assemblies
Perl
25
star
16

ekidna

Assembly based core genome SNP alignments for bacteria
Perl
25
star
17

sixess

๐Ÿ”ฌ๐Ÿ› Rapid 16s rRNA identification from isolate FASTQ files
Shell
23
star
18

cgmlst-dists

๐Ÿปโ‡”๐Ÿจ Calculate distance matrix from ChewBBACA cgMLST allele call tables
C
23
star
19

PEAR

Pair-End AssembeR
C
22
star
20

mokka

Annotate your metagenome assemblies
11
star
21

scapper

Whole genome core alignments from multiple draft genomes
Perl
10
star
22

kounta

๐Ÿงฎ ๐Ÿ”ข Generate multi-sample k-mer count matrix from WGS
Perl
9
star
23

trencha

Normalize VCF depth for Illumina GC bias
Perl
7
star
24

legsta

๐Ÿ—โญ In silico Legionella pneumophila Sequence Based Typing
Perl
7
star
25

snasm

Assembly based core SNP alignments
Perl
7
star
26

tseemann.github.io

Torsten Seemann's Home Page
HTML
7
star
27

noary

๐Ÿฃ ๐Ÿฆ A lightweight nucleotide bacterial ortholog clustering tool
Perl
7
star
28

wombac

โ€ผ๏ธ Rapid core genome SNP alignments from multiple bacterial genomes
Perl
7
star
29

klosham

Find closest aligned sequences to a query sequnece
C
6
star
30

kopynumba

Identify copy number variation in bacterial Illumina sequences
6
star
31

fasterqc

A non-Java alternative to the classic FastQC tool
Perl
5
star
32

ragnarokka

Annotate and correct erro-prone ONT genomes
5
star
33

spekki

Species prediction from NGS reads
Python
5
star
34

polisha

Fix small assembly errors using Illumina reads
Perl
5
star
35

polyfix

๐Ÿ”ชโ›“๏ธ Repair nanopore assemblies using related genome(s)
Perl
5
star
36

varion

5
star
37

injecta

Insert genes into genomes to aid synthetic test data generation
Perl
4
star
38

kurra

Fast whole genome phylogeny
4
star
39

heterik

Estimate heterozygosity or mixture level of a bacterial WGS sample
4
star
40

dehomopolymerate

Collapse sequence homopolymers to a single character
C
4
star
41

babykraken

๐Ÿ‘ถ๐Ÿฆ‘ Very small Kraken2 database for bundling with pipelines
4
star
42

bowkaster

cgMLST from FASTQ reads
4
star
43

perl-biotool

๐Ÿซ ๐Ÿช Small pure Perl5 libraries for writing command line bioinformatics tools
Perl
3
star
44

anthrakks

Distinguish Bacillus cereus and biovar anthracis (anthrax)
3
star
45

bioinfo-scripts

Collection of bioinformatics utility scripts, mostly written in Bioperl
Perl
3
star
46

gbk2bcfgff

Convert Genbank to GFF compatible with "bcftools csq"
2
star
47

easy-web-blast

2
star
48

mini-outbreak

Small WGS dataset for testing bacterial outbreak analysis pipelines
2
star
49

snippa

Experimental modular bacterial SNP calling pipeline
Perl
2
star
50

vikka

Viral genomics toolkit for pandemics
1
star
51

gard

๐Ÿ† ๐Ÿ’Š Gonococcal Antimicrobial Resistance Detection
1
star
52

wtfq

Duplicate FASTQ reads to address undersequenced regions
C
1
star
53

simuvar

Simulate variants of bacterial genomes for testing SNP callers
1
star
54

coginator

Assign COGs to protein sequences
1
star
55

skrilla

It ain't all about skrilla
1
star
56

arborkart

Phylogenomic trees with maps for the web
1
star
57

assembill

Simple script to clip, assemble, tile and annotate a bacterial genome from Illumina reads
Shell
1
star
58

kroucha

Mock repository for Sanger publications citing Croucher et al
1
star