23 skills found
marbl / ParsnpParsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
JiaoLaboratory / CRAQIdentification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement
BirolLab / NtEdit✏️ Genome assembly polishing & SNV detection
combogenomics / MedusaA draft genome scaffolder that uses multiple reference genomes in a graph-based approach.
nf-core / GenomeannotatorPipeline for the identification of (coding) gene structures in draft genomes.
ohlab / GRiDGrowth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x).
simoncchu / GAPPadderGAPPadder is tool for closing gaps on draft genomes with short sequencing data
EnzoAndree / FastMLST⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies
combogenomics / CONTIGuatorBacterial genomes finishing tool for structural insights on draft genomes
carolzhou / MultiPhATEThroughput PhATE processing of draft or finished phage genomes
tseemann / ScapperWhole genome core alignments from multiple draft genomes
QuentinRougemont / EASYstratagenome annotation (RNAseq and TE) pipeline (draft)
kammoji / GapFinisherA reliable gap filling pipeline for draft genomes
khyox / DraftGenomesScript to collect sequence files from multiple NCBI WGS projects and process them (LEGACY SOFTWARE)
thackl / Cross Species ScaffoldingSuper-scaffolding of draft genome assemblies with in silico mate-pair libraries derived from (closely) related references
EverymanBio / PestalotiopsisAssembly and phylogentic analysis pipeline for draft genome of a Pestalotiopsis fungi.
oist / Plessy PairwiseGenomeComparisonDraft workflow for pairwise genome comparison. We recommend you use the new nf-core version instead: https://nf-cor.e/pairgenomealign
SysBioChalmers / Hanpo GEMDraft genome-scale model of Hansenula polymorpha (Ogataea polymorpha; Pichia angusta)
lazzarigioele / GempipeThis is gempipe, a tool for drafting, curating and analyzing pan and multi-strain genome-scale metabolic models (GSMMs or GEMs).
BirolLab / GapPredictCharacter-level language model for draft genome assembly gap-filling
