Sequencing pack#

This page is generated from the code and must not be edited by hand.

Library types, platforms, read structure, processing steps and measures.

Senses: 48
Spellings: 270
Kinds of thing: format, instrument, read_structure, statistic, technique
Pack: sequencing version 2, by Ingence, under the MIT licence
Digest of its words: 3e6fe571255ad9253914c2fd0593d201

Words#

Spelling	Means	Kind	Notes
`10x`	single cell rna (`single_cell_rna`)	`technique`
`16s`	metagenomics (`metagenomics`)	`technique`
`4c`	conformation (`conformation`)	`technique`
`5c`	conformation (`conformation`)	`technique`
`_1`	read one (`read_one`)	`read_structure`
`_2`	read two (`read_two`)	`read_structure`
`ab1`	capillary sequencing trace (`capillary_trace`)	`format`
`adapterremoval`	trimming (`trimming`)	`technique`
`align`	alignment (`alignment`)	`technique`
`aligned`	alignment (`alignment`)	`technique`	also spelled by aligned (stage)
`alignmentrate`	mapping rate (`mapping_rate`)	`statistic`
`aln`	multiple alignment format (`multiple_alignment_format`)	`format`
`amplicon`	dna sequencing (`dna_sequencing`)	`technique`
`amplicon_16s`	metagenomics (`metagenomics`)	`technique`
`anndata`	matrix format (`matrix_format`)	`format`
`annotate`	annotation tool (`annotation_tool`)	`technique`
`annovar`	annotation tool (`annotation_tool`)	`technique`
`assembled`	assembly (`assembly`)	`technique`
`assembly`	assembly (`assembly`)	`technique`
`atac-seq`	chromatin (`chromatin`)	`technique`
`atacseq`	chromatin (`chromatin`)	`technique`
`augustus`	annotation tool (`annotation_tool`)	`technique`
`bai`	alignment format (`alignment_format`)	`format`
`bam`	alignment format (`alignment_format`)	`format`
`barcode`	barcode (`barcode`)	`read_structure`
`barcode_read`	index read (`index_read`)	`read_structure`
`basequality`	quality score (`quality_score`)	`statistic`
`bcf`	variant format (`variant_format`)	`format`
`bcftools_call`	variant calling (`variant_calling`)	`technique`
`bcl2fastq`	demultiplexed (`demultiplexed`)	`technique`
`bclconvert`	demultiplexed (`demultiplexed`)	`technique`
`bed`	interval format (`interval_format`)	`format`
`bedgraph`	interval format (`interval_format`)	`format`
`bgi`	other platform (`other_platform`)	`instrument`
`bigwig`	interval format (`interval_format`)	`format`
`bisulfite`	methylation (`methylation`)	`technique`
`bowtie`	alignment (`alignment`)	`technique`
`bowtie2`	alignment (`alignment`)	`technique`
`breadth`	coverage (`coverage`)	`statistic`
`broadpeak`	interval format (`interval_format`)	`format`
`bw`	interval format (`interval_format`)	`format`
`bwa`	alignment (`alignment`)	`technique`
`canu`	assembly (`assembly`)	`technique`
`capturec`	conformation (`conformation`)	`technique`
`cell_id`	flowcell (`flowcell`)	`read_structure`
`chip-seq`	chromatin (`chromatin`)	`technique`
`chipseq`	chromatin (`chromatin`)	`technique`
`clip-seq`	crosslinking (`crosslinking`)	`technique`
`clipped`	trimming (`trimming`)	`technique`
`clipseq`	crosslinking (`crosslinking`)	`technique`
`contig`	assembly (`assembly`)	`technique`
`contigs`	assembly (`assembly`)	`technique`
`countmatrix`	read count (`read_count`)	`statistic`
`coverage`	coverage (`coverage`)	`statistic`
`cpm`	normalised expression (`normalised_expression`)	`statistic`
`crai`	alignment format (`alignment_format`)	`format`
`cram`	alignment format (`alignment_format`)	`format`
`cufflinks`	quantification tool (`quantification_tool`)	`technique`
`cut-and-run`	chromatin (`chromatin`)	`technique`
`cutadapt`	trimming (`trimming`)	`technique`
`cutandrun`	chromatin (`chromatin`)	`technique`
`cutandtag`	chromatin (`chromatin`)	`technique`
`dedup`	deduplication (`deduplication`)	`technique`
`deduplicated`	deduplication (`deduplication`)	`technique`
`deepvariant`	variant calling (`variant_calling`)	`technique`
`degs`	differential expression (`differential_expression`)	`technique`
`demultiplexed`	demultiplexed (`demultiplexed`)	`technique`
`demux`	demultiplexed (`demultiplexed`)	`technique`
`depth`	coverage (`coverage`)	`statistic`
`deseq`	differential expression (`differential_expression`)	`technique`
`deseq2`	differential expression (`differential_expression`)	`technique`
`deseq_norm`	normalised expression (`normalised_expression`)	`statistic`
`diffexp`	differential expression (`differential_expression`)	`technique`
`diffexpr`	differential expression (`differential_expression`)	`technique`
`dnase`	chromatin (`chromatin`)	`technique`
`dnaseq`	dna sequencing (`dna_sequencing`)	`technique`
`dropseq`	single cell rna (`single_cell_rna`)	`technique`
`dualindex`	barcode (`barcode`)	`read_structure`
`eclip`	crosslinking (`crosslinking`)	`technique`
`edger`	differential expression (`differential_expression`)	`technique`
`element_bio`	other platform (`other_platform`)	`instrument`
`embl`	annotation format (`annotation_format`)	`format`
`emseq`	methylation (`methylation`)	`technique`
`exome`	dna sequencing (`dna_sequencing`)	`technique`
`fa`	read format (`read_format`)	`format`
`faa`	read format (`read_format`)	`format`
`faireseq`	chromatin (`chromatin`)	`technique`
`fasta`	read format (`read_format`)	`format`
`fastp`	trimming (`trimming`)	`technique`
`fastq`	read format (`read_format`)	`format`
`fastqc`	quality control (`quality_control`)	`technique`
`fc`	flowcell (`flowcell`)	`read_structure`	also spelled by fold change (statistic)
`featurecounts`	quantification tool (`quantification_tool`)	`technique`
`flowcell`	flowcell (`flowcell`)	`read_structure`
`flye`	assembly (`assembly`)	`technique`
`fna`	read format (`read_format`)	`format`
`forward`	read one (`read_one`)	`read_structure`
`fpkm`	normalised expression (`normalised_expression`)	`statistic`
`fq`	read format (`read_format`)	`format`
`freebayes`	variant calling (`variant_calling`)	`technique`
`fsa`	read format (`read_format`)	`format`
`fwd`	read one (`read_one`)	`read_structure`
`gatk`	variant calling (`variant_calling`)	`technique`
`gb`	annotation format (`annotation_format`)	`format`	read only as a file extension, after a dot
`gbk`	annotation format (`annotation_format`)	`format`
`genbank`	annotation format (`annotation_format`)	`format`
`genrich`	peak calling (`peak_calling`)	`technique`
`gff`	annotation format (`annotation_format`)	`format`
`gff3`	annotation format (`annotation_format`)	`format`
`gridion`	long read platform (`long_read_platform`)	`instrument`
`gtf`	annotation format (`annotation_format`)	`format`
`gvcf`	variant format (`variant_format`)	`format`
`h5ad`	matrix format (`matrix_format`)	`format`
`haplotypecaller`	variant calling (`variant_calling`)	`technique`
`hi-c`	conformation (`conformation`)	`technique`
`hic`	conformation (`conformation`)	`technique`
`hifi`	long read platform (`long_read_platform`)	`instrument`
`hisat`	alignment (`alignment`)	`technique`
`hisat2`	alignment (`alignment`)	`technique`
`hiseq`	short read platform (`short_read_platform`)	`instrument`
`homer_peaks`	peak calling (`peak_calling`)	`technique`
`htseq`	quantification tool (`quantification_tool`)	`technique`
`i1`	index read (`index_read`)	`read_structure`
`i2`	index read (`index_read`)	`read_structure`
`i5`	barcode (`barcode`)	`read_structure`
`i7`	barcode (`barcode`)	`read_structure`
`iclip`	crosslinking (`crosslinking`)	`technique`
`illumina`	short read platform (`short_read_platform`)	`instrument`
`index_read`	index read (`index_read`)	`read_structure`
`index_seq`	barcode (`barcode`)	`read_structure`
`ion-torrent`	other platform (`other_platform`)	`instrument`
`iontorrent`	other platform (`other_platform`)	`instrument`
`iseq`	short read platform (`short_read_platform`)	`instrument`
`its`	metagenomics (`metagenomics`)	`technique`
`kallisto`	alignment (`alignment`)	`technique`
`l001`	lane (`lane`)	`read_structure`
`l002`	lane (`lane`)	`read_structure`
`l003`	lane (`lane`)	`read_structure`
`l004`	lane (`lane`)	`read_structure`
`lane`	lane (`lane`)	`read_structure`
`lanes`	lane (`lane`)	`read_structure`
`limma`	differential expression (`differential_expression`)	`technique`
`loom`	matrix format (`matrix_format`)	`format`
`macs`	peak calling (`peak_calling`)	`technique`
`macs2`	peak calling (`peak_calling`)	`technique`
`macs3`	peak calling (`peak_calling`)	`technique`
`maf`	variant format (`variant_format`)	`format`
`mapping-rate`	mapping rate (`mapping_rate`)	`statistic`
`mappingrate`	mapping rate (`mapping_rate`)	`statistic`
`mapq`	quality score (`quality_score`)	`statistic`
`markdup`	deduplication (`deduplication`)	`technique`
`meandepth`	coverage (`coverage`)	`statistic`
`megahit`	assembly (`assembly`)	`technique`
`merfish`	spatial transcriptomics (`spatial_transcriptomics`)	`technique`
`metagenome`	metagenomics (`metagenomics`)	`technique`
`metagenomics`	metagenomics (`metagenomics`)	`technique`
`methylation_array`	methylation (`methylation`)	`technique`
`methylseq`	methylation (`methylation`)	`technique`
`mgi`	other platform (`other_platform`)	`instrument`
`micro_c`	conformation (`conformation`)	`technique`
`minimap`	alignment (`alignment`)	`technique`
`minimap2`	alignment (`alignment`)	`technique`
`minion`	long read platform (`long_read_platform`)	`instrument`
`miseq`	short read platform (`short_read_platform`)	`instrument`
`mrnaseq`	rna sequencing (`rna_sequencing`)	`technique`
`msa`	multiple alignment format (`multiple_alignment_format`)	`format`
`mtx`	matrix format (`matrix_format`)	`format`
`multimapped`	mapping rate (`mapping_rate`)	`statistic`
`multiqc`	quality control (`quality_control`)	`technique`
`mutect`	variant calling (`variant_calling`)	`technique`
`nanopore`	long read platform (`long_read_platform`)	`instrument`
`narrowpeak`	interval format (`interval_format`)	`format`
`nextera`	short read platform (`short_read_platform`)	`instrument`
`nextseq`	short read platform (`short_read_platform`)	`instrument`
`novaseq`	short read platform (`short_read_platform`)	`instrument`
`ont`	long read platform (`long_read_platform`)	`instrument`
`pacbio`	long read platform (`long_read_platform`)	`instrument`
`paired`	paired end (`paired_end`)	`read_structure`
`paired-end`	paired end (`paired_end`)	`read_structure`
`pairedend`	paired end (`paired_end`)	`read_structure`
`panel_seq`	dna sequencing (`dna_sequencing`)	`technique`
`parclip`	crosslinking (`crosslinking`)	`technique`
`pe`	paired end (`paired_end`)	`read_structure`
`peaks`	peak calling (`peak_calling`)	`technique`
`phred`	quality score (`quality_score`)	`statistic`
`picard_metrics`	quality control (`quality_control`)	`technique`
`polya_seq`	rna sequencing (`rna_sequencing`)	`technique`
`prokka`	annotation tool (`annotation_tool`)	`technique`
`promethion`	long read platform (`long_read_platform`)	`instrument`
`q20`	quality score (`quality_score`)	`statistic`
`q30`	quality score (`quality_score`)	`statistic`
`qc_report`	quality control (`quality_control`)	`technique`
`qualimap`	quality control (`quality_control`)	`technique`
`r1`	read one (`read_one`)	`read_structure`	read only in a file of the type `read_format`
`r2`	read two (`read_two`)	`read_structure`	read only in a file of the type `read_format`; also spelled by r squared (statistic)
`rawcounts`	read count (`read_count`)	`statistic`
`rds_matrix`	matrix format (`matrix_format`)	`format`
`read1`	read one (`read_one`)	`read_structure`
`read2`	read two (`read_two`)	`read_structure`
`readcount`	read count (`read_count`)	`statistic`
`rev_read`	read two (`read_two`)	`read_structure`
`reverse`	read two (`read_two`)	`read_structure`
`revio`	long read platform (`long_read_platform`)	`instrument`
`ribo-seq`	ribosome profiling (`ribosome_profiling`)	`technique`
`riboseq`	ribosome profiling (`ribosome_profiling`)	`technique`
`ripseq`	crosslinking (`crosslinking`)	`technique`
`rlog`	normalised expression (`normalised_expression`)	`statistic`
`rmdup`	deduplication (`deduplication`)	`technique`
`rna-seq`	rna sequencing (`rna_sequencing`)	`technique`
`rnaseq`	rna sequencing (`rna_sequencing`)	`technique`
`rpkm`	normalised expression (`normalised_expression`)	`statistic`
`rrbs`	methylation (`methylation`)	`technique`
`rsem`	quantification tool (`quantification_tool`)	`technique`
`run_folder`	flowcell (`flowcell`)	`read_structure`
`runid`	flowcell (`flowcell`)	`read_structure`
`salmon`	alignment (`alignment`)	`technique`
`sam`	alignment format (`alignment_format`)	`format`
`sc-rna-seq`	single cell rna (`single_cell_rna`)	`technique`
`scaffold`	assembly (`assembly`)	`technique`
`scrnaseq`	single cell rna (`single_cell_rna`)	`technique`
`se`	single end (`single_end`)	`read_structure`	also spelled by standard error (statistic)
`seacr`	peak calling (`peak_calling`)	`technique`
`seq`	provider sequence text (`sequence_text`)	`format`	read only as a file extension, after a dot
`seqfish`	spatial transcriptomics (`spatial_transcriptomics`)	`technique`
`shotgun_meta`	metagenomics (`metagenomics`)	`technique`
`single-cell rna sequencing`	single cell rna (`single_cell_rna`)	`technique`
`single-cell rna-seq`	single cell rna (`single_cell_rna`)	`technique`
`single-cell transcriptomics`	single cell rna (`single_cell_rna`)	`technique`
`single-end`	single end (`single_end`)	`read_structure`
`singleend`	single end (`single_end`)	`read_structure`
`sleuth`	differential expression (`differential_expression`)	`technique`
`slideseq`	spatial transcriptomics (`spatial_transcriptomics`)	`technique`
`smartseq`	single cell rna (`single_cell_rna`)	`technique`
`snpeff`	annotation tool (`annotation_tool`)	`technique`
`snrnaseq`	single cell rna (`single_cell_rna`)	`technique`
`spades`	assembly (`assembly`)	`technique`
`spatial`	spatial transcriptomics (`spatial_transcriptomics`)	`technique`
`split_by_sample`	demultiplexed (`demultiplexed`)	`technique`
`sra`	read format (`read_format`)	`format`
`star_aligner`	alignment (`alignment`)	`technique`
`sto`	multiple alignment format (`multiple_alignment_format`)	`format`
`stockholm`	multiple alignment format (`multiple_alignment_format`)	`format`
`strelka`	variant calling (`variant_calling`)	`technique`
`stringtie`	quantification tool (`quantification_tool`)	`technique`
`targeted`	dna sequencing (`dna_sequencing`)	`technique`
`tenx`	single cell rna (`single_cell_rna`)	`technique`
`tophat`	alignment (`alignment`)	`technique`	declared ambiguous with background subtraction (technique)
`totalrna`	rna sequencing (`rna_sequencing`)	`technique`
`tpm`	normalised expression (`normalised_expression`)	`statistic`
`tracking_ribosome`	ribosome profiling (`ribosome_profiling`)	`technique`
`trim`	trimming (`trimming`)	`technique`
`trimmed`	trimming (`trimming`)	`technique`	also spelled by cropped (stage)
`trimmomatic`	trimming (`trimming`)	`technique`
`ultima`	other platform (`other_platform`)	`instrument`
`umi`	barcode (`barcode`)	`read_structure`
`umi_dedup`	deduplication (`deduplication`)	`technique`
`unique-molecular-identifier`	barcode (`barcode`)	`read_structure`
`uniquelymapped`	mapping rate (`mapping_rate`)	`statistic`
`variants`	variant calling (`variant_calling`)	`technique`
`vcf`	variant format (`variant_format`)	`format`
`vep`	annotation tool (`annotation_tool`)	`technique`
`visium`	spatial transcriptomics (`spatial_transcriptomics`)	`technique`
`voom`	differential expression (`differential_expression`)	`technique`
`vst`	normalised expression (`normalised_expression`)	`statistic`
`wes`	dna sequencing (`dna_sequencing`)	`technique`
`wgbs`	methylation (`methylation`)	`technique`
`wgs`	dna sequencing (`dna_sequencing`)	`technique`
`wig`	interval format (`interval_format`)	`format`
`x-coverage`	coverage (`coverage`)	`statistic`
`xenium_class`	spatial transcriptomics (`spatial_transcriptomics`)	`technique`