Sequencing services

The Natural Resources Institute Finland (Luke) is procuring Sequencing services as specified in this invitation to tender and its appendices. SUBJECT OF THE PROCUREMENT This framework arrangement covers Sequencing services as defined in this invitation to tender and its appendices. Luke is looking for suppliers for the following services: 1) Metagenomic sequences short and long reads 2) Transcriptomic short reads 3) Transcriptomic long reads with ≥Q30 (80%) 4) Amplicon and metabarcoding short reads 5) Amplicon and metabarcoding long reads with ≥Q30 (80%) 6) Sanger sequencing 7) Whole genome sequencing short reads 8) Whole genome sequencing long reads 9) Sequencing of self-made pooled libraries short reads (medium through put) 10) Sequencing of self-made pooled libraries short reads (high through put) 11) Sequencing of self-made pooled libraries short reads (low through put) 12) Sequencing of self-made pooled libraries long reads with ≥Q30 (80%) 13) ATAC Interested suppliers can take part in either one or all of the service packages. The scope of the procurement is described in more detail particularly in Annex 1 "Description of the procurement"., 1. Metagenomic sequencing short and long reads Supplier for sequencing services for metagenomic sequences. (DNA extracted from e.g. soil, water, ice, snow, plant air traps/root/stem, gut of the organism.) Target is metagenomic sequencing and sequencing library preparation. Both Long reads (PacBio or similar) and short reads (Illumina/AVITI or similar) or combination of this are part of this procurement. Maximum turnaround time is 4 weeks. Turnaround time begins when the supplier has received the sample and has checked the sample quality (quality check must be done within 2 workdays). Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready. Maximum turnaround time applies when there are equal or less than 192 samples. If there are more than 192 samples the supplier must give estimation of the turnaround time., 2. Transcriptomic short reads Provider for sequencing services for transcriptomic. (RNA extracted from e.g. different tissues of plant or animals or soil.) Transcriptomic library preparation using totalRNA as starting material for e.g. total RNA metatranscriptomics, gene expression profiling, rRNA depletion or Poly A (+) RNA enrichment , lncRNA, miRNA. Sequencing of libraries using Illumina/AVITI or similar or Pac-Bio or similar. Maximum turnaround time is 4 weeks. Turnaround time begins when the supplier has received the sample and has checked the sample quality (quality check must be done within 2 workdays). Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready. Maximum turnaround time applies when there are equal or less than 192 samples. If there are more than 192 samples the supplier must give estimation of the turnaround time., 4. Amplicon and metabarcoding short reads Provider for sequencing services for amplicons and metabarcoding from various sources. (The sample matrix is DNA or eDNA.), including: a. Fungi b. Bacteria c. Animals, protozoa, microscopic animals d. Animal droppings (mammalian identification) e. Plants Amplicons and metabarcoding. PCR of gene of interest, including but not limited to 16S rRNA, 18S rRNA, COI, ITS from bacteria, archaea, fungi, protist, fish, mammals, insects. Maximum turnaround time is 4 weeks. Turnaround time begins when the supplier has received the sample and has checked the sample quality (quality check must be done within 2 workdays). Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready. Maximum turnaround time applies when there are equal or less than 192 samples. If there are more than 192 samples the supplier must give estimation of the turnaround time., 6. Sanger sequencing Provider for sequencing services for Sanger sequencing of PCR-fragments and plasmids. Maximum turnaround time is 2 weeks. Turnaround time begings when the supplier has received the sample. Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready., 7. Whole genome sequencing short reads Provider for sequencing services for whole genome sequencing. a. Viruses (DNA, RNA) b. Viruses with host (DNA and RNA) c. Bacteria d. Fungi e. Plants f. Animals Maximum turnaround time is 3 weeks. Turnaround time begings when the supplier has received the sample. Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready. Maximum turnaround time applies when there are equal or less than 5 samples. If there are more than 5 samples the supplier must give estimation of the turnaround time., 9. Sequencing of self-made pooled libraries short reads (medium through put) Provider for sequencing services for sequencing of self-made pooled libraries. Sequencing of libraries which customer has prepared (e.g. metagenomes, genomes, amplicons, metatranscriptomes transcriptome etc.) using short read (Illumina, AVITI or similar). Maximum turnaround time is 3 weeks. Turnaround time begins when the supplier has received the sample. Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready., 3. Transcriptomic long reads with =Q30 (80%) Provider for sequencing services for transcriptomic. (RNA extracted from e.g. different tissues of plant or animals or soil.) Transcriptomic library preparation using totalRNA as starting material for e.g. total RNA metatranscriptomics, gene expression profiling, rRNA depletion or Poly A (+) RNA enrichment , lncRNA, miRNA. Sequencing of libraries using Illumina/AVITI or similar or Pac-Bio or similar. Maximum turnaround time is 4 weeks. Turnaround time begins when the supplier has received the sample and has checked the sample quality (quality check must be done within 2 workdays). Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready. Maximum turnaround time applies when there are equal or less than 8 samples. If there are more than 8 samples the supplier must give estimation of the turnaround time. Minimum of Q30 as a quality measure., 5. Amplicon and metabarcoding long reads with =Q30 (80%) Provider for sequencing services for amplicons and metabarcoding from various sources. (The sample matrix is DNA or eDNA.), including: a. Fungi b. Bacteria c. Animals, protozoa, microscopic animals d. Animal droppings (mammalian identification) e. Plants Amplicons and metabarcoding. PCR of gene of interest, including but not limited to 16S rRNA, 18S rRNA, COI, ITS from bacteria, archaea, fungi, protist, fish, mammals, insects. Maximum turnaround time is 4 weeks. Turnaround time begins when the supplier has received the sample and has checked the sample quality (quality check must be done within 2 workdays). Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready. Maximum turnaround time applies when there are equal or less than 192 samples. If there are more than 192 samples the supplier must give estimation of the turnaround time. Minimum of Q30 as a quality measure., 8. Whole genome sequencing long reads Provider for sequencing services for whole genome sequencing. a. Viruses (DNA, RNA) b. Viruses with host (DNA and RNA) c. Bacteria d. Fungi e. Plants f. Animals Maximum turnaround time is 3 weeks. Turnaround time begins when the supplier has received the sample. Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready. Maximum turnaround time applies when there are equal or less than 5 samples. If there are more than 5 samples the supplier must give estimation of the turnaround time., 10. Sequencing of self-made pooled libraries short reads (high through put) Provider for sequencing services for sequencing of self-made pooled libraries. Sequencing of libraries which customer has prepared (e.g. metagenomes, genomes, amplicons, metatranscriptomes transcriptome etc.) using short read (Illumina, AVITI or similar). Maximum turnaround time is 3 weeks. Turnaround time begins when the supplier has received the sample. Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready., 13. ATAC Provider for sequencing services for ATAC. Maximum turnaround time is 4 weeks. Turnaround time begings when the supplier has received the sample and has checked the sample quality (quality check must be done within 2 workdays). Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready., 11. Sequencing of self-made pooled libraries short reads (low through put) Provider for sequencing services for sequencing of self-made pooled libraries. Sequencing of libraries which customer has prepared (e.g. metagenomes, genomes, amplicons, metatranscriptomes transcriptome etc.) using short read (Illumina, AVITI or similar). Maximum turnaround time is 3 weeks. Turnaround time begins when the supplier has received the sample. Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready., 12. Sequencing of self-made pooled libraries long reads with =Q30 (80%) Provider for sequencing services for sequencing of self-made pooled libraries. Sequencing of libraries which customer has prepared (e.g. metagenomes, genomes, amplicons, metatranscriptomes transcriptome etc.) using long read (PacBio or similar). Maximum turnaround time is 3 weeks. Turnaround time begings when the supplier has received the sample. Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready., Lot 1: 1. Metagenomic sequencing short and long reads Supplier for sequencing services for metagenomic sequences. (DNA extracted from e.g. soil, water, ice, snow, plant air traps/root/stem, gut of the organism.) Target is metagenomic sequencing and sequencing library preparation. Both Long reads (PacBio or similar) and short reads (Illumina/AVITI or similar) or combination of this are part of this procurement. Maximum turnaround time is 4 weeks. Turnaround time begins when the supplier has received the sample and has checked the sample quality (quality check must be done within 2 workdays). Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready. Maximum turnaround time applies when there are equal or less than 192 samples. If there are more than 192 samples the supplier must give estimation of the turnaround time. Lot 2: 2. Transcriptomic short reads Provider for sequencing services for transcriptomic. (RNA extracted from e.g. different tissues of plant or animals or soil.) Transcriptomic library preparation using totalRNA as starting material for e.g. total RNA metatranscriptomics, gene expression profiling, rRNA depletion or Poly A (+) RNA enrichment , lncRNA, miRNA. Sequencing of libraries using Illumina/AVITI or similar or Pac-Bio or similar. Maximum turnaround time is 4 weeks. Turnaround time begins when the supplier has received the sample and has checked the sample quality (quality check must be done within 2 workdays). Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready. Maximum turnaround time applies when there are equal or less than 192 samples. If there are more than 192 samples the supplier must give estimation of the turnaround time. Lot 3: 4. Amplicon and metabarcoding short reads Provider for sequencing services for amplicons and metabarcoding from various sources. (The sample matrix is DNA or eDNA.), including: a. Fungi b. Bacteria c. Animals, protozoa, microscopic animals d. Animal droppings (mammalian identification) e. Plants Amplicons and metabarcoding. PCR of gene of interest, including but not limited to 16S rRNA, 18S rRNA, COI, ITS from bacteria, archaea, fungi, protist, fish, mammals, insects. Maximum turnaround time is 4 weeks. Turnaround time begins when the supplier has received the sample and has checked the sample quality (quality check must be done within 2 workdays). Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready. Maximum turnaround time applies when there are equal or less than 192 samples. If there are more than 192 samples the supplier must give estimation of the turnaround time. Lot 4: 6. Sanger sequencing Provider for sequencing services for Sanger sequencing of PCR-fragments and plasmids. Maximum turnaround time is 2 weeks. Turnaround time begings when the supplier has received the sample. Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready. Lot 5: 7. Whole genome sequencing short reads Provider for sequencing services for whole genome sequencing. a. Viruses (DNA, RNA) b. Viruses with host (DNA and RNA) c. Bacteria d. Fungi e. Plants f. Animals Maximum turnaround time is 3 weeks. Turnaround time begings when the supplier has received the sample. Turnaround time ends when the supplier has completed the sequencing and notified that the results are ready. Maximum turnaround time applies when there are equal or less than 5 samples. If there are more than 5 samples the supplier must give estimation of the turnaround time. CPV: 73110000 73111000 Organisation: Luonnonvarakeskus (Natural Resources Institute Finland) Procedure: open