malariagen / pipelines
Pipelines for processing malaria parasite and mosquito genome sequence data.
☆14Updated 6 months ago
Alternatives and similar repositories for pipelines:
Users that are interested in pipelines are comparing it to the libraries listed below
- A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies☆34Updated 10 months ago
- ☆28Updated 10 months ago
- Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads☆24Updated this week
- A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remo…☆18Updated last week
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes☆35Updated 4 years ago
- Influenza genome analysis Nextflow workflow☆22Updated last month
- MIRA sequence assembler☆29Updated 4 months ago
- PhyloCSF++ computes PhyloCSF tracks for whole-genome multiple sequence alignments, scores single MSA, annotates CDS features in GFF/GTF f…☆31Updated 3 years ago
- Toolkit for preparing genomes for submission to NCBI☆29Updated 3 years ago
- This repository hosts a large collection of Nextflow snippets☆57Updated 3 months ago
- BigSeqKit: a parallel Big Data toolkit to process FASTA and FASTQ files at scale☆55Updated last year
- Assembler for raw de novo genome assembly of long uncorrected reads.☆37Updated 5 years ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 6 years ago
- Influenza genome analysis Nextflow workflow☆26Updated 3 weeks ago
- 🔗Genome assembly scaffolder using minimizer graphs☆83Updated 7 months ago
- Whole Exome/Whole Genome Sequencing alignment pipeline☆28Updated 7 months ago
- create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks☆44Updated 9 months ago
- SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.☆24Updated last year
- Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads☆59Updated 8 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆41Updated 4 years ago
- ⛰ covtobed | Convert the coverage track from a BAM file into a BED file☆44Updated 3 years ago
- ☆27Updated 2 months ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆39Updated 2 years ago
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆44Updated 4 months ago
- More realistic simulator for genomic DNA sequences from Illumina machines that achieves a similar k-mer spectrum as the original☆52Updated 2 years ago
- perSVade: personalized Structural Variation detection☆39Updated 2 months ago
- vembrane filters VCF records using python expressions☆58Updated last week
- ☆27Updated 3 years ago
- Protein Alignment and Detection Interface☆61Updated last year
- showTree can visualize the phylogeny, protein sequences and protein domains of a gene family in one figure.☆30Updated 6 years ago