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181 search results found
Vcftools
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415
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
Prokka
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415
โก โ Rapid prokaryotic genome annotation
Snippy
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408
โ๏ธ โก Rapid haploid variant calling and core genome alignment
Edta
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294
Extensive de-novo TE Annotator
Braker
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293
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
Roary
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219
Rapid large-scale prokaryote pan genome analysis
Gaas
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188
Genome Assembly and Annotation Service code
Metabolic
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148
A scalable high-throughput metabolic and biogeochemical functional trait profiler
Novoplasty
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140
NOVOPlasty - The organelle assembler and heteroplasmy caller
Mcscanx
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135
MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
Mirdeep2
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120
Discovering known and novel miRNAs from small RNA sequencing data
Shovill
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104
โกโ ๏ธ Assemble bacterial isolate genomes from Illumina paired-end reads
Biopieces
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102
Biopieces is a bioinformatic framework of tools easily used and easily created.
Get_homologues
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98
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
Metamaps
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88
Long-read metagenomic analysis
Nullarbor
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80
๐พ ๐ "Reads to report" for public health and clinical microbiology
Mitobim
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74
MITObim - mitochondrial baiting and iterative mapping
Scrnaseqpipeline
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73
Gms
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70
The Genome Modeling System installer
Multi Metagenome
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65
Scripts and tutorials on how to assemble individual microbial genomes from metagenomes
Genome
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62
Core modules used by the GMS
Feelnc
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61
FEELnc : FlExible Extraction of LncRNA
Pirate
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58
A toolbox for pangenome analysis and threshold evaluation.
Simug
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58
simuG: a general-purpose genome simulator
Wengan
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57
An accurate and ultra-fast hybrid genome assembler
Jupiterplot
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54
A Circos-based tool to visualize genome assembly consistency
Synima
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53
Synteny Imager
Bigsdb
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53
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
Estimate_genome_size.pl
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53
Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
Alitv
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52
Visualize whole genome alignments as linear maps
Clinsv
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51
Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
Hera
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49
Gbrowse
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48
the Generic Genome Browser
Retroseq
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43
RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
Snpsplit
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43
Allele-specific alignment sorting
Cgpbattenberg
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41
Battenberg algorithm and associated implementation script
Blobology
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40
Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step (NO LONGER MANTAINED)
Fast Plast
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40
Automated de novo assembly of whole chloroplast genomes.
Get_phylomarkers
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39
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
Gawn
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37
Genome Annotation Without Nightmares
Cnvcaller
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37
Kraken_db_install_scripts
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36
Updated Kraken DB install scripts to cope with new-ish NCBI structure
Novograph
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36
NovoGraph: building whole genome graphs from long-read-based de novo assemblies
Circleator
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32
Flexible circular visualization of genome-associated data with BioPerl and SVG.
Mtbseq_source
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32
MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.
Transposome
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30
A toolkit for annotation of transposable element families from unassembled sequence reads
Cld
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30
A software for the multispecies design of CRISPR/Cas9 libraries
Pgcgap
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29
The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline
Mitoseek
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29
Seeking information like heteroplasmy, structure variants, etc. on Mitochondrial genome from next generation sequencing
Rnaseq
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28
RNASeq pipeline
Lrsday
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27
LRSDAY: Long-read Sequencing Data Analysis for Yeasts
Diffreps
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27
Differential analysis for ChIP-seq with biological replicates
Islandpath
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27
IslandPath standalone software
Bitacora
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27
BITACORA: A Bioinformatics tool for gene family annotation
16gt
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26
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Tephra
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26
A tool for discovering transposable elements and describing patterns of genome evolution
Ebcall
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26
an empirical Bayesian framework for mutation detection from cancer genome sequencing data
Datasets
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25
Benchmark datasets for WGS analysis
Cgppindel
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25
Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
Dna Me Pipeline
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24
DCC/DAC methylation pipeline source
Organelle_pba
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23
A software to assemble chloroplast and mitochodrial genomes using PacBio data
Genelosspipe
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22
Microbedb
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22
Provides a local database of in-house and published genomes for Bacteria and Archaea from NCBI
Parsing Repeatmasker Outputs
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21
Few scripts facilitating the extraction of info from Repeat Masker .out files
Piggy
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20
Pipeline for analysing intergenic regions in bacteria
2brad_denovo
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20
Genome-wide de novo genotyping with 2bRAD
Exstra
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20
Expanded STR algorithm for Illumina sequencing data
Ratite Genomics
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19
Scripts and other material for the assembly and analysis of ratite genomes.
Ekidna
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19
Assembly based core genome SNP alignments for bacteria
Pga
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19
Plastid Genome Annotator
Cegma_v2
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18
The final version 2 release of our software to detect core genes in eukaryotic genomes
Plasmidseeker
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18
A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
Wgs2ncbi
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18
Toolkit for preparing genomes for submission to NCBI
Nextflow Annotate
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18
Workflows I find helpful for fungal genome annotation
Ani
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17
Calculate Average Nucleotide Identity (ANI) for prokaryotic genomes
23andme Impute
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17
Scripts and advice to run IMPUTE2 on 23 and me raw data
Om Hic Scaffolding
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17
Workflows for correcting and scaffolding long-read (PacBio, nanopore) genome assemblies using optical mapping and/or Dovetail Hi-C data
Binning
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16
Scripts required to calculate tetramer frequencies and create input files for ESOM. See: Dick, G.J., A. Andersson, B.J. Baker, S.S. Simmons, B.C. Thomas, A.P. Yelton, and J.F. Banfield (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biology, 10: R85
Get_jgi_genomes
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16
A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.
Cld_docker
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16
Docker for CRISPR Library Designer | https://genomebiology.biomedcentral.com/articles/1
Gal
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16
Genome Annotation Library - A perl toolkit for working with SO compliant genome annotations
Pseudohaploid
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16
Create a pseudohaploid assembly from a partially resolved diploid assembly
Sars_cov_2
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15
Bioinformatics analysis of SARS-CoV-2
Tgnet
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15
Transcript to Genome Consistency Network
Khaper
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15
Sesbio
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14
Bioinformatics scripts for genome analysis
Phastaf
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14
Identify phage regions in bacterial genomes for masking purposes
Gcluster
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14
A simple-to-use tool for visualizing and comparing genome contexts for numerous genomes
Parsecnv2
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14
Parse Copy Number Variation from Array and Sequencing
Pokay
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13
Report salient qPCR primer/probe or immune epitope mismatches info against a set of pathogen isolate genomes
Ppspcp
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13
A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline
Sequence Scripts
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12
Random utility scripts for genomics data
Metaplotr
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12
A Perl/R pipeline for plotting metagenes
Pangenomepipeline
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12
PanGenomePipeline
Mfannot
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12
MFannot is a program for the annotation of mitochondrial and plastid genomes
Eztree
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12
A Perl pipeline for identifying marker genes and build phylogenetic trees for a set of genomes
Appris
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12
Annotating principal splice isoforms
Typete
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12
Genotyping of segregating mobile elements insertions
Berokka
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12
๐ ๐ซ Trim, circularise and orient long read bacterial genome assemblies
Ervcaller
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11
ERVcaller is a tool designed to accurately detect and genotype non-reference unfixed endogenous retroviruses (ERVs) and other transposable elements (TEs) in the human genome using next-generation sequencing (NGS) data. We evaluated the tools using both simulated and real benchmark whole-genome sequencing (WGS) datasets. ERVcaller is capable to accurately detect various TE insertions of any lengths, particularly ERVs. It allows for the use of a TE reference library regardless of sequence complexi
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