Update UniVec database. Remove duplicates from oxford_nanopore.fasta

CHANGELOG.rst

@@ -7,6 +7,10 @@ Changelog
 .. This document is user facing. Please word the changes in such a way
 .. that users understand how the changes affect the new version.
 
+version 0.12.0-dev
+------------------
++ Update internal UniVec database to version from November 21st 2023.
+
 version 0.11.1
 ------------------
 + Fix a memory leak that occurred in Python 3.12 due to a refcounting API

src/sequali/contaminants/README

@@ -9,11 +9,12 @@ Other sources of contaminations are:
 Source : (https://www.ncbi.nlm.nih.gov/tools/vecscreen/contam/
 
 NCBI keeps a database called UniVec for vectors and updated. It was last
-updated on May 5th 2017. It can be downloaded from:
+updated on November 21st 2023. It can be downloaded from:
 https://ftp.ncbi.nlm.nih.gov/pub/UniVec
 
 The UniVec database contains many adapters, linkers, and primers but not yet
-a lot of those that are used in Oxford nanopore sequencing. The
+a lot of those that are used in Oxford nanopore sequencing. As of 2023
+some nanopore Adapters have been added. The
 oxford_nanopore.fasta file provides the sequences as represented in the
 technical documentation. All possible barcoding sequencing adapters for
 nanopore have not yet been added.

src/sequali/contaminants/UniVec.fasta

@@ -27103,3 +27103,44 @@ GCGCTTTTGGCGAACCTTCTCGCATTAGCTGCGTTGTGCATATTGGCGATGGTG
 >gnl|uv|A08585.1:1-86 pMG36 expression vector DNA sequence
 ATGGCAATCGTTTCAGCAGAAAAATTCGTAATTCGAGCTCGCCCGGGGATCGATCCTCTAGAGTCGACCT
 GCAGGCATGCAAGCTT
+>gnl|uv|NGB01098.1:1-61 Oxford Nanopore Technologies Sequencing Adapter Y_top
+GGCGTCTGCTTGGGTGTTTAACCTTTTTTTTTTAATGTACTTCGTTCAGTTACGTATTGCT
+>gnl|uv|NGB01099.1:1-22 Oxford Nanopore Technologies Sequencing Adapter Y_bottom
+GCAATACGTAACTGAACGAAGT
+>gnl|uv|NGB01100.1:1-15 Oxford Nanopore Technologies PCR Barcoding Kit (SQK-PBK004) 5' primer top
+ATCGCCTACCGTGAC
+>gnl|uv|NGB01101.1:1-29 Oxford Nanopore Technologies PCR Barcoding Kit (SQK-PBK004) 3' primer top
+TTAACCTACTTGCCTGTCGCTCTATCTTC
+>gnl|uv|NGB01102.1:1-22 Oxford Nanopore Technologies PCR Barcoding Kit (SQK-PBK004) 3' primer bottom
+TTTCTGTTGGTGCTGATATTGC
+>gnl|uv|NGB01103.1:1-30 Oxford Nanopore Technologies Direct RNA Sequencing Kit (SQK-RNA002) RT Adapter top
+GGCTTCTTCTTGCTCTTAGGTAGTAGGTTC
+>gnl|uv|NGB01104.1:1-49 Oxford Nanopore Technologies Direct RNA Sequencing Kit (SQK-RNA002) RT Adapter bottom
+GAGGCGAGCGGTCAATTTTCCTAAGAGCAAGAAGAAGCCTTTTTTTTTT
+>gnl|uv|NGB01105.1:1-31 Oxford Nanopore Technologies Direct RNA Sequencing Kit (SQK-RNA002) RNA Adapter Mix Top
+TTTTTTTTTTTTTATGATGCAAGATACGCAC
+>gnl|uv|NGB01106.1:1-76 Oxford Nanopore Technologies Direct RNA Sequencing Kit (SQK-RNA002) RNA Adapter Mix Bottom
+GAGGCGAGCGGTCAATTTGCAATATCAGCACCAACAGAAACAACCATCGTCTATCCCTCATCATCAGAAC
+CTACTA
+>gnl|uv|NGB01107.1:1-36 Oxford Nanopore Technologies Ligation Sequencing Kit (SQK-LSK114) Ligation Adaptor Y Top
+TTTTTTTTCCTGTACTTCGTTCAGTTACGTATTGCT
+>gnl|uv|NGB01108.1:1-27 Oxford Nanopore Technologies Ligation Sequencing Kit (SQK-LSK114) Ligation Adaptor Y Bottom
+GCAATACGTAACTGAACGAAGTACAGG
+>gnl|uv|NGB01109.1:1-26 PacBio ULI gDNA amplification adapter
+AAGCAGTGGTATCAACGCAGAGTACT
+>gnl|uv|NGB01110.1:1-19 Illumina Nextera-Illumina PCR Kit Adapter Read 1-Read 2
+CTGTCTCTTATACACATCT
+>gnl|uv|NGB01111.1:1-16 Illumina DNA PCR-Free Tagmentation Adapter
+ATGTGTATAAGAGACA
+>gnl|uv|NGB01112.1:1-19 Nextera Mate Pair Adapter
+AGATGTGTATAAGAGACAG
+>gnl|uv|NGB01113.1:1-33 Illumina TruSeq UD/CD Adapter Trimming Read 1
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+>gnl|uv|NGB01114.1:1-33 Illumina TruSeq UD/CD Adapter Trimming Read 2
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+>gnl|uv|NGB01115.1:1-21 Illumina TruSeq Small RNA Adapter Trimming Read
+TGGAATTCTCGGGTGCCAAGG
+>gnl|uv|NGB01116.1:1-19 Illumina TruSeq RNA 5' Adapter RA5
+GCAGAGCACAGCCGACGAC
+>gnl|uv|NGB01117.1:1-21 Illumina TruSeq RNA 3' Adapter RA3
+TGGAATTCTCGGGTGCCAAGG

src/sequali/contaminants/oxford_nanopore.fasta

@@ -1,21 +1,9 @@
->Oxford nanopore ligation kit or rapid adapter, top strand
-TTTTTTTTCCTGTACTTCGTTCAGTTACGTATTGCT
->Oxford nanopore ligation kit, bottom strand
-GCAATACGTAACTGAACGAAGTACAGG
 >Oxford nanopore Strand Switching Primer II (SSPII)
 TTTCTGTTGGTGCTGATATTGCTTT
 >Oxford nanopore RT Primer (RTP)
 CTTGCCTGTCGCTCTATCTTCAGAGGAG
 >Oxford nanopore cDNA RT Adapter (CRT)
 CTTGCGGGCGGCGGACTCTCCTCTGAAGATAGAGCGACAGGCAAG
->Oxford nanopore RT Adapter (RTA), top strand
-GGCTTCTTCTTGCTCTTAGGTAGTAGGTTC
->Oxford nanopore RT Adapter (RTA), bottom strand
-GAGGCGAGCGGTCAATTTTCCTAAGAGCAAGAAGAAGCCTTTTTTTTTT
->Oxford nanopore RNA Adapter Mix (RMX), top strand
-TTTTTTTTTTTTTATGATGCAAGATACGCAC
->Oxford nanopore RNA Adapter Mix (RMX), bottom strand
-GAGGCGAGCGGTCAATTTGCAATATCAGCACCAACAGAAACAACCATCGTCTATCCCTCATCATCAGAACCTACTA
 >Oxford nanopore CDNA primer, forward sequence
 ATCGCCTACCGTGACAAGAAAGTTGTCGGTGTCTTTGTGACTTGCCTGTCGCTCTATCTTC
 >Oxford nanopore CDNA primer, reverse sequence
@@ -24,10 +12,6 @@ ATCGCCTACCGTGACAAGAAAGTTGTCGGTGTCTTTGTGTTTCTGTTGGTGCTGATATTGC
 ACTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTT
 >Oford nanopore Strand Switching Primer (SSP)
 TTTCTGTTGGTGCTGATATTGCTGGG
->Oxford nanopore Adapter Mix (AMX), top strand
-TTTTTTTTTTAATGTACTTCGTTCAGTTACGTATTGCT
->Oxford nanopore Adapter Mix (AMX), bottom strand
-GCAATACGTAACTGAACGAAGT
 >Oxford nanopore Native Adapter (NA), top strand
 TTTTTTTTCCTGTACTTCGTTCAGTACGTATTGCT
 >Oxford nanopore Native Adapter (NA), bottom strand