Abstract: The present invention provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example.

Abstract: Described herein are high coverage single tube Long Fragment Read (stLFR) technology which uses performs stLFR on target DNA fragments that have already been amplified before they are co-barcoded, which provides higher amount of DNA for sequencing and increases sequencing coverage. In some embodiments, the high coverage stLFR described in this application uses two rounds of stLFR. In some embodiments, the target DNA fragments are transposed with transposons having particular positional barcodes that can be used to order sequence reads.

Abstract: This disclosure provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example.

Abstract: The present invention provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example.

Abstract: The methods and compositions disclosed herein relate to preparing libraries to sequence long molecules comprising repetitive regions. In some embodiments, this strategy involves substituting selected nucleotides in each molecule to predetermined, different nucleotides at low frequencies in random positions and co-barcoding the molecule in single-tube LFR reactions to generate mutagenized barcoded fragments. Each mutagenized barcoded fragment comprises a barcode, and the barcode comprises a barcode sequence.

Abstract: This application relates to methods and compositions for preparing a library of polynucleotides for sequencing comprises in a single reaction mixture. The method comprises contacting a double-stranded target nucleic acid with one or more nicking agents to produce overlapping nucleic acid fragments separated by staggered single-stranded breaks; and contacting a partially double-stranded first adapter with at least one of the nucleic acid fragments in the presence of a ligase, thereby ligating the 5? terminus of the double-stranded region of the first adapter to the 3? terminus of the at least one of the nucleic acid fragments using a DNA ligase via 3? branch ligation. The first adapter comprises (i) a double-stranded blunt end having a 5? terminus and a 3? terminus and (ii) a single-stranded region comprising a barcode.

Abstract: Disclosed herein are DNA sequencing methods involving applying a long DNA molecule to an indexed array comprising an array of transfer sites (TS). Each TS comprises a substrate and a source of clonal barcodes (SCB) attached to or situated on the substrate. Each SCB comprises many copies of a unique transferable barcode sequence, and the unique transferable barcode sequence associated with each TS is known. The unique transferable barcode sequence is transferred from the SCB portion of the TS to a location on the long DNA molecule. DNA fragments comprising the barcode sequences are recovered from the array and sequenced. Sequence reads from these fragments are assembled based on the relative positions of the TS on the array.

Abstract: This disclosure provides methods and compositions for long fragment read sequencing. Technology is described for preparing long fragments of genomic DNA, for processing genomic DNA for long fragment read sequencing methods, as well as software and algorithms for processing and analyzing sequence data. Combinatorial oligonucleotide bar codes are used to label fragments from nearby portions of the genome, which facilitate computational assembly of sequence reads to obtain the genome sequence. This improves efficiency and accuracy of sequencing, whereby an entire sequence can be obtained from fragments that constitute a lower coverage amount of the genome.

Abstract: The present invention is directed to methods and compositions for long fragment read sequencing. The present invention encompasses methods and compositions for preparing long fragments of genomic DNA, for processing genomic DNA for long fragment read sequencing methods, as well as software and algorithms for processing and analyzing sequence data.

Abstract: Described herein are high coverage single tube Long Fragment Read (stLFR) technology which uses performs stLFR on target DNA fragments that have already been amplified before they are co-barcoded, which provides higher amount of DNA for sequencing and increases sequencing coverage. In some embodiments, the high coverage stLFR described in this application uses two rounds of stLFR. In some embodiments, the target DNA fragments are transposed with transposons having particular positional barcodes that can be used to order sequence reads.

Abstract: Methods and compositions for preparing a nucleic acid sequencing library are described including (a)transposing an insertion sequence into first fragments of the target nucleic acid, wherein the insertion sequence comprises a hybridization sequence, and wherein the transposing produces nicks in the first fragments; (b) combining in a single mixture (i) the first fragments of the target nucleic acid from (a), (ii) a splint oligonucleotide, and (iii) a population of beads, wherein each bead comprises capture oligonucleotides immobilized thereon, and (c) ligating capture oligonucleotides of individual beads to inserted hybridization sequences of individual first fragments.

Abstract: The present invention provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example.

Abstract: Long fragment read techniques can be used to identify deletions and resolve base calls by utilizing shared labels (e.g., shared aliquots) of a read with any reads corresponding to heterozygous loci (hets) of a haplotype. For example, the linking of a locus to a haplotype of multiple hets can increase the reads available at the locus for determining a base call for a particular haplotype. For a hemizygous deletion, a region can be linked to one or more hets, and the labels for a particular haplotype can be used to identify which reads in the region correspond to which haplotype. In this manner, since the reads for a particular haplotype can be identified, a hemizygous deletion can be determined. Further, a phasing rate of pulses can be used to identify large deletions. A deletion can be identified with the phasing rate is sufficiently low, and other criteria can be used.

Abstract: The present invention provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example.

Abstract: This disclosure provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example.

Abstract: The present invention provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example.

Abstract: This disclosure provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example.

Abstract: The present invention is directed to methods and compositions for long fragment read sequencing. The present invention encompasses methods and compositions for preparing long fragments of genomic DNA, for processing genomic DNA for long fragment read sequencing methods, as well as software and algorithms for processing and analyzing sequence data.

Abstract: This disclosure provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example.

Abstract: The present invention is directed to logic for analysis of nucleic acid sequence data that employs algorithms that lead to a substantial improvement in sequence accuracy and that can be used to phase sequence variations, e.g., in connection with the use of the long fragment read (LFR) process.