bennuru's repositories
asgart
A genome-scale, fast, and precise segmental duplications mapping tool
Bandage
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
centromere_seeker
bash script to search for centromeric repeat patterns in PacBio data, using several current tools (trf and R)
deepTools
Tools to process and analyze deep sequencing data.
Filtlong
quality filtering tool for long reads
finishingTool
finshingTool
forACT
Pipeline to prepare alignments for visualization with ACT (goo.gl/1T28jX) and for locating possible inter-chromosomal re-arrengments/misjoints
gff-rename
Replace sequence_IDs in gff3 based on given genome.fasta
jcvi
Python utility libraries on genome assembly, annotation and comparative genomics
Long-read-genome-assembly
Genome assembly using ONT and PacBio data
LongStitch
Correct and scaffold assemblies using long reads
mimeo
Scan genomes for internally repeated sequences, elements which are repetitive in another species, or high-identity HGT candidate regions between species.
MpGAP
Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
nanome
NANOME(Nanopore methylation) pipeline of DNA methylation calling tools for Oxford Nanopore sequencing
nemADSQ
A repository containing pipelines for nematode genome assembly, decontamination, scaffolding, and QC
Ostracoda_genomes
Code for "First annotated draft genomes of non-marine ostracods (Ostracoda, Crustacea) with different reproductive modes" manuscript.
otipu_chrom_assem
Scripts and files associated with the chromosomal assembly of O. tipulae manuscript
PEPPI
Pipeline for protein-protein interaction prediction
phip-flow
A Nextflow pipeline to align, merge, and organize large PhIP-Seq datasets
Pipeliner
Pipeliner Program
RagTag
Tools for fast and flexible genome assembly scaffolding and improvement
telomeric-identifier
Identify and find telomeres, or telomeric repeats in a genome.
TRF2GFF
Convert Tandem Repeat Finder dat file output into gff3 format