Alternatives and similar repositories for AliNe

Users that are interested in AliNe are comparing it to the libraries listed below

• nf-core / detaxizer
  A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remo…
  ☆22Updated this week
• KamilSJaron / k-mer-approaches-for-biodiversity-genomics
  k-mer learning materials
  ☆80Updated 9 months ago
• nf-core / genomeassembler
  Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
  ☆30Updated 3 weeks ago
• kjenike / panagram
  ☆67Updated 2 weeks ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆55Updated 4 months ago
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆63Updated last year
• nextgenusfs / funannotate2
  Eukaryotic genome annotation software.
  ☆20Updated 2 weeks ago
• mribeirodantas / NextflowSnippets
  This repository hosts a large collection of Nextflow snippets
  ☆56Updated 9 months ago
• PombertLab / SYNY
  The SYNY pipeline investigates synteny between species by reconstructing protein clusters from gene pairs.
  ☆46Updated 4 months ago
• yangao07 / longcallD
  A local-haplotagging-based small and structural variant caller
  ☆89Updated this week
• genomeannotation / GAG
  Generates an NCBI .tbl file of annotations on a genome.
  ☆68Updated 7 years ago
• alignoth / alignoth
  Creating alignment plots from bam files
  ☆67Updated this week
• OLF-Bioinformatics / VariantDetective
  Identify short variants and structural variants from raw sequencing data or genomic sequences
  ☆33Updated last year
• harta55 / EnTAP
  EnTAP is moving to GitLab for future changes https://gitlab.com/PlantGenomicsLab/EnTAP
  ☆41Updated 9 months ago
• katerinakazantseva / strainy
  Graph-based assembly phasing
  ☆90Updated 6 months ago
• dwinter / pafr
  Read, manipulate and visualize 'Pairwise mApping Format' data in R
  ☆75Updated 4 years ago
• NBISweden / EMBLmyGFF3
  An efficient way to convert gff3 annotation files into EMBL format ready to submit.
  ☆64Updated 3 months ago
• naturalis / wgs2ncbi
  Toolkit for preparing genomes for submission to NCBI
  ☆29Updated 4 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆33Updated 11 months ago
• lh3 / longdust
  Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome
  ☆81Updated this week
• thackl / minidot
  Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2
  ☆76Updated 9 years ago
• SouthGreenPlatform / culebrONT
  A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.
  ☆36Updated 7 months ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆42Updated 3 weeks ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 2 months ago
• AliTVTeam / AliTV
  Visualize whole genome alignments as linear maps
  ☆73Updated 3 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated 2 months ago
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆63Updated 5 years ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• gear-genomics / dicey
  In-silico PCR, primer design and padlock design for in-situ sequencing
  ☆51Updated 3 months ago
• BioinformaticsToolsmith / Identity
  ☆34Updated last year