aidenlab / 3d-dna
3D de novo assembly (3D DNA) pipeline
☆203Updated 9 months ago
Related projects: ⓘ
- PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.☆249Updated 2 months ago
- ☆184Updated last month
- Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads☆187Updated 2 months ago
- Fast and accurately polish the genome generated by long reads.☆205Updated 10 months ago
- Fast and accurate de novo assembler for long reads☆358Updated 4 months ago
- MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!☆219Updated last year
- Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data☆123Updated 2 years ago
- Tool to plot synteny and structural rearrangements between genomes☆276Updated 3 months ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆170Updated 8 months ago
- Generate an interactive dot plot from mummer or minimap alignments☆189Updated 8 months ago
- Synteny and Rearrangement Identifier☆322Updated last week
- Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling☆233Updated last month
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆175Updated 4 months ago
- (Not Offical) BBMap short read aligner, and other bioinformatic tools.☆208Updated 3 years ago
- Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)☆125Updated last year
- PASA software☆172Updated 9 months ago
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆183Updated last month
- Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads☆106Updated last year
- RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.☆226Updated this week
- Any Way to Show Multi genomic Synteny☆152Updated 2 months ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆199Updated 2 months ago
- pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…☆257Updated 10 months ago
- Extensive de-novo TE Annotator☆334Updated last week
- NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…☆287Updated 6 months ago
- Ultra-fast de novo assembler using long noisy reads☆129Updated 3 years ago
- Read trimming tool for Illumina NGS data.☆127Updated 9 years ago
- Scan contig files against PubMLST typing schemes☆192Updated last year
- quality filtering tool for long reads☆275Updated last year
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆283Updated this week
- Nanopore demultiplexing, QC and alignment pipeline☆169Updated 3 weeks ago