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181 search results found
Sneakernet
⭐
11
🐾 QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
Clipseqtools
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11
A suite for the analysis of CLIP-Seq datasets.
Defining_genomic_regions
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11
Define regions in the genome
Computational Genome Analysis
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11
Website for Computational Exome and Genome Analysis
Gc_content_in_sliding_window
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11
Calculate GC% and GC deviation for circular genomes
Genome Fingerprints
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11
Software for creating and comparing genome fingerprints.
Positive Selection
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10
Scripts and procedures for detecting positively selected genes and codons in primates
Irys Scaffolding
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10
scripts to parse IrysView output
Damidseq_pipeline
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10
An automated pipeline for processing DamID sequencing datasets
Bugbuilder
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10
Hands-free microbial genome assembly
Amos
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10
A clone of the official AMOS git repo on sourceforge: https://sourceforge.net/projects/amos/
Mpd C
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10
Multiplex Primer Design
Bioscripts
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10
a bucket of bioinformatics scripts
Wgddetector
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10
Soprano
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10
SelectiOn in PRotein ANnotated regiOns. Adapted dN/dS based method to detect selection in specific protein regions
Circsplice
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9
CircSplice
Fgmp
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9
Fungal Genome Mapping Pipeline
Goatassemblyscripts
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9
A loose collection of scripts and utilities for processing and analyzing the Goat reference genome assembly
Pogenom
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9
Population genomics from metagenomes
Trna Read Mapping
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9
Biogrinder
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9
Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
Calc_switcherr
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8
Tabsat
⭐
8
Targeted Amplicon Bisulfite Sequencing Analysis Tool
Gmata
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8
Software GMATA for SSR mining, marker designing, genotyping, plot etc.
Vicaller
⭐
8
A software to detect virome-wide integrations
Magpy
⭐
8
Snakemake pipeline for annotating metagenome-assembled genomes (MAGs) (pronounced mag-pie)
Relocate
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8
Find the locations of TEs using the TSD in unassembled short reads by comparing to a closely related reference genome assembly
Fast Gep
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8
Fast genealogical relationship evaluation of bacterial isolates with WGS data.
Restrictiondigest
⭐
8
A powerful Perl module for simulating the genome digestions by restriction enzymes
Eahelitron
⭐
8
Easy to Annotate Helitrons Unix-like command line.
Rec Genome Tools
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8
Plethora
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8
Copy number estimation of highly duplicated sequences
Scubat
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8
Scaffolding Contigs Using Blat And Transcripts
Genomon Itdetector
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8
for detecting internal tandem duplication from genome sequence data.
Garlic
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8
FakeSequence is an artificial non-functional realistic DNA sequence generator.
Tiger
⭐
8
Target / Integrative Genetic Element Retriever: precisely maps IGEs (a defined type of genomic island) in bacterial and archaeal genomes; package also includes orthogonal program Islander
J.nome.s
⭐
7
A lightweight genome browser entirely written in javascript.
Varathon
⭐
7
A scalable variant calling and benchmarking framework supporting both short and long reads.
Hicres
⭐
7
Estimating and predicting HiC library resolution
Dinumt
⭐
7
Circos Pipeline
⭐
7
circos pipeline
Trackhub Registry
⭐
7
Specifications and implementation of the TrackHub registry
Vagrent
⭐
7
A toolset for comparing genomic variants to reference genome annotation to identify potential biological consequences
Gsmer
⭐
7
Strain/species identification in metagenomes using genome-specific markers
Parallellastz
⭐
7
parallelLastz: Running Lastz in parallel
Strandscript
⭐
7
Scaffolder Evaluation
⭐
7
Wrapper scripts to run genome assembly scaffolding tools and scripts to analyse the output for accuracy.
Bio Graphics
⭐
7
Generate GD images of biological sequences and annotations
Phylogenomics Tools
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6
Scripts for automating tasks in phylogenetics with microbial genomes
Oxford Plots
⭐
6
eHive pipeline to build pairwise Oxford plots
Oga
⭐
6
Organelle Genome Assembler
Mario
⭐
6
Measurement of Allelic Ratio Informatics Operator (MARIO) pipeline
Pangloss
⭐
6
Pangenome analysis of eukaryotes.
Epiteome
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6
Simultaneous Detection of Transposable Element Insertion Sites and their DNA Methylation Levels from Plant Genomes
Genome Data Of Hanfu Apple
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6
FASTA files of chromosomes and genes, gff files for gene models.
Autocirc
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6
A computational toolkit of fast and automatical identification of back-splice junctions of potential circular RNAs (circRNAs) from RNA-seq data.
Diya
⭐
6
Repository for DIYA code
Potion
⭐
6
POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes
Fastqsifter
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6
Separate contaminating reads from FASTQ files (e.g., mitochondria, symbionts, bacterial or human contaminants)
Withncbi
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6
egaz and alignDB work with external (NCBI/EBI) data
Brumir
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6
BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data.
Cg Pipeline
⭐
6
Genome assembly/prediction/annotation pipeline for the Linux command line
Wombac
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6
‼️ Rapid core genome SNP alignments from multiple bacterial genomes
Genomemining
⭐
6
Methodologies for genome mining and annotation
Genome_annotation
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6
The genome annotation service provides automated gene annotation based on the RAST system. This deploys both client and service components.
Clustcompare
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5
Pipeline to compare secondary metabolite biosynthetic gene clusters (BGCs)
Genotype Fingerprints
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5
Scapper
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5
Whole genome core alignments from multiple draft genomes
Scallopadvising
⭐
5
Mirna Mrna_integration
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5
A detailed guide to analise and integrate small-RNASeq and RNASeq samples using miARma-Seq
Ephagen
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5
Estimate NGS Dataset qualitity in terms of its ability to detect mutations of predefined spectrum
Ssrmmd
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5
SSRMMD: A Rapid and Accurate Algorithm for Mining SSR Feature Loci and Candidate Polymorphic SSRs Based on Assembled Sequences.
Alienomics
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5
Automated pipeline for HGT and contaminant detection in an assembled, annotated genome
Isoblat
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5
use RNA transcripts to assess assembly - this program parses the output of a BLAT run of transcriptome vs. a genome. It returns 1) Total % mapped, 2) average %coverage of a mapping, and 3) number of transcripts mapping to a single contig/scaffold. It is simple to run. Just run the blat (transcripts vs. genome) and then run the script with the blat-output and your transcript-fasta-file as arguments.
Ensembl Database Loader
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5
A eHive Pipeline for loading Ensembl and Ensembl Genomes databases to a MySQL compatible server
Ensembl Metadata
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5
API for storing and querying metadata from Ensembl and EnsemblGenomes
Otagogalaxy
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5
1000 genomes and Merriman Lab Galaxy
Liftover Utils
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5
Utilities for lifting over genome coordinates in C. elegans
Bng Fragilesiterepair
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5
Scripts for repairing (stitching) fragile sites of BioNano genome maps.
Blast2ogmsa
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5
Whole organelle genome-wide alignment construction method, which ultilizes BLAST tool, to facilitate phylogeny analysis
Genomealign
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5
Genefamilyanalysis
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5
Compute gene families for a set of genomes.
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101-181 of 181 search results
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