|
nf-core/abacas
|
genome
assembly
contiguate
|
Contiguate draft genome assembly
|
|
nf-core/abra2
|
alignment
realignment
indels
bam
dna
rna
splice-junctions
assembly
|
Assembly Based ReAligner for next-generation sequencing data
|
|
nf-core/abricate/run
|
bacteria
assembly
antimicrobial resistance
|
Screen assemblies for antimicrobial resistance against multiple databases
|
|
nf-core/abricate/summary
|
bacteria
assembly
antimicrobial reistance
|
Screen assemblies for antimicrobial resistance against multiple databases
|
|
nf-core/abritamr/run
|
bacteria
fasta
antibiotic resistance
|
A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes
|
|
nf-core/abyss/abysspe
|
genome
assembly
genome assembler
short reads
de novo assembler
|
ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.
|
|
nf-core/adapterremoval
|
trimming
adapters
merging
fastq
|
Trim sequencing adapters and collapse overlapping reads
|
|
nf-core/adapterremovalfixprefix
|
adapterremoval
fastq
dedup
|
Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.
|
|
nf-core/admixture
|
ancestry
population genetics
admixture
reference panels
gwas
|
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).
|
|
nf-core/affy/justrma
|
affy
microarray
expression
matrix
|
Read CEL files into an ExpressionSet and generate a matrix
|
|
nf-core/agat/convertbed2gff
|
genome
bed
gff
conversion
|
Takes a bed12 file and converts to a GFF3 file
|
|
nf-core/agat/convertgff2bed
|
genome
bed
gff
conversion
|
Takes a GFF3 file and converts to a bed12 file
|
|
nf-core/agat/convertspgff2gtf
|
genome
gff
gtf
conversion
|
Converts a GFF/GTF file into a proper GTF file
|
|
nf-core/agat/convertspgff2tsv
|
genome
gff
gtf
conversion
tsv
|
Converts a GFF/GTF file into a TSV file
|
|
nf-core/agat/convertspgxf2gxf
|
genome
gff
gtf
conversion
|
Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file
|
|
nf-core/agat/spaddintrons
|
gtf
gff
introns
|
Add intron features to gtf/gff file without intron features.
|
|
nf-core/agat/spextractsequences
|
genomics
gff
extract
fasta
sequence
feature
|
This script extracts sequences in fasta format according to features described
in a gff file.
|
|
nf-core/agat/spfilterbyorfsize
|
genomics
GFF/GTF
filter
annotation
|
The script reads a gff annotation file, and create two output files, one contains the gene models with ORF passing the test, the other contains the rest. By default the test is "> 100" that means all gene models that have ORF longer than 100 Amino acids, will pass the test.
|
|
nf-core/agat/spfilterfeaturefromkilllist
|
genomics
gff
remove
feature
|
The script aims to remove features based on a kill list. The default behaviour is to look at the features's ID.
If the feature has an ID (case insensitive) listed among the kill list it will be removed. /!\ Removing a level1
or level2 feature will automatically remove all linked subfeatures, and removing all children of a feature will
automatically remove this feature too.
|
|
nf-core/agat/spflagshortintrons
|
genomics
gtf
gff
intron
short
annotation
|
The script flags the short introns with the attribute <pseudo>. Is is usefull to avoid ERROR when submiting the data to EBI.
(Typical EBI error message: ********ERROR: Intron usually expected to be at least 10 nt long. Please check the accuracy)
|