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cellgeni/fetch10xmeta
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metadata
GEO
SRA
ENA
ArrayExpress
BioProject
10x
single-cell
public data
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Fetches and parses metadata for public 10x datasets from GEO (GSE*), ArrayExpress (E-MTAB*), or BioProject (PRJ*). Downloads raw metadata from SRA/ENA/BioStudies, resolves sample-to-run mappings, classifies each run by download type, and produces a merged links file.
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cellgeni/hmetacells
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metacells
hierarchical-clustering
single-cell
scRNA-seq
scATAC-seq
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Hierarchical metacell aggregation for single-cell genomics data.
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cellgeni/irods/getmetadata
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irods
metadata
csv
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Module to get metadata from an iRODS collections and data objects and output as CSV
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cellgeni/seacells
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metacells
single-cell
scRNA-seq
scATAC-seq
aggregation
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SEACells aggregates single-cell profiles into metacells from scRNA-seq or scATAC-seq data.
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nf-core/abacas
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genome
assembly
contiguate
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Contiguate draft genome assembly
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nf-core/abra2
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alignment
realignment
indels
bam
dna
rna
splice-junctions
assembly
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Assembly Based ReAligner for next-generation sequencing data
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nf-core/abricate/run
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bacteria
assembly
antimicrobial resistance
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Screen assemblies for antimicrobial resistance against multiple databases
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nf-core/abricate/summary
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bacteria
assembly
antimicrobial reistance
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Screen assemblies for antimicrobial resistance against multiple databases
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nf-core/abritamr/run
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bacteria
fasta
antibiotic resistance
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A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes
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nf-core/abyss/abysspe
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genome
assembly
genome assembler
short reads
de novo assembler
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ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.
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nf-core/adapterremoval
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trimming
adapters
merging
fastq
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Trim sequencing adapters and collapse overlapping reads
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nf-core/adapterremovalfixprefix
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adapterremoval
fastq
dedup
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Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.
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nf-core/admixture
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ancestry
population genetics
admixture
reference panels
gwas
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ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study).
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nf-core/affy/justrma
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affy
microarray
expression
matrix
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Read CEL files into an ExpressionSet and generate a matrix
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nf-core/agat/convertbed2gff
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genome
bed
gff
conversion
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Takes a bed12 file and converts to a GFF3 file
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nf-core/agat/convertgff2bed
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genome
bed
gff
conversion
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Takes a GFF3 file and converts to a bed12 file
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nf-core/agat/convertspgff2gtf
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genome
gff
gtf
conversion
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Converts a GFF/GTF file into a proper GTF file
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nf-core/agat/convertspgff2tsv
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genome
gff
gtf
conversion
tsv
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Converts a GFF/GTF file into a TSV file
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nf-core/agat/convertspgxf2gxf
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genome
gff
gtf
conversion
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Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file
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nf-core/agat/spaddintrons
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gtf
gff
introns
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Add intron features to gtf/gff file without intron features.
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