clemgoub / dnaPipeTE
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X)…
☆54Updated 2 years ago
Alternatives and similar repositories for dnaPipeTE:
Users that are interested in dnaPipeTE are comparing it to the libraries listed below
- ☆43Updated 8 years ago
- PhyloAcc a software to detect the changes of conservation of a genomic region☆30Updated last week
- ☆77Updated last month
- meta-pipeline for repetitive element de-fragmentation and annotation☆24Updated 4 years ago
- TSEBRA: Transcript Selector for BRAKER☆47Updated 4 months ago
- Synteny Imager☆61Updated 7 months ago
- Few scripts facilitating the extraction of info from Repeat Masker .out files☆79Updated 3 years ago
- A program to call variants from genome alignment☆79Updated last year
- A fast tool for detecting and decomposing segmental duplications in genome assemblies☆47Updated last year
- A shiny application to visualize MCscan result☆36Updated 2 years ago
- Show pangenome graphs in an easy way☆55Updated 2 years ago
- A (very) simple script to QC Hi-C data.☆25Updated 3 months ago
- De novo annotation of young retrotransposons☆48Updated 2 years ago
- A tool for evaluate long-read de novo assembly results☆44Updated 7 months ago
- Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement☆58Updated 2 months ago
- Neural network classification of TE☆87Updated 2 years ago
- ☆24Updated last month
- TGS scaffolding☆46Updated 3 years ago
- Pipelines and tools for the processing of ancient and modern HTS data.☆47Updated 2 weeks ago
- Splitting of sequence reads by internal adapter sequence search☆51Updated last year
- A python script for finding telomeric repeats (TTAGGG/CCCTAA) in FASTA files☆33Updated 2 years ago
- Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com…☆31Updated 6 months ago
- Generates an NCBI .tbl file of annotations on a genome.☆66Updated 7 years ago
- Pipeline to convert a haploid assembly into diploid☆100Updated 2 months ago
- A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats☆65Updated 3 years ago
- Python wrappers for programs that search for transposable elements☆19Updated 8 years ago
- Tools for working with second gen assemblies, fasta sequences, etc☆93Updated 8 years ago
- Simple pileup-based variant caller☆87Updated last month
- Converts a VCF file to a FASTA alignment provided a reference genome and a GFF file☆49Updated 5 months ago
- Conditional Reciprocal Best Blast☆42Updated 8 years ago