Search Results for "pacbio"
Sort By:
Showing 19 open source projects for "pacbio"
View related business solutions-
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
-
Veeam Data Platform v13.1 - Get Your Free TrialTry Veeam Data Platform today. Experience the unified platform that's secure by design, portable by default, and proven to recover clean, fast, and anywhere.
-
1
IsoQuant
Transcript discovery and quantification with long RNA reads
IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores. IsoQuant allows reconstructing and quantifying transcript models with high precision and decent recall. If the reference annotation is given, IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. IsoQuant further performs annotated gene, isoform, exon, and intron quantification. -
2
BBMap
BBMap short read aligner, and other bioinformatic tools.
...All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels. Very fast. BBNorm: Kmer-based error-correction and normalization tool. Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity. Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s. ... -
3
misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee that all files are the version used in the analysis. ... -
4
...Additionally reads may be simulated using the genomes of all indivdiuals in the population as template. Reads may be simulated using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). SimulaTE will greatly aid in evaluating the suitability of different approaches for estimating TE abundance within populations and to test whether given genomic resources, such as a reference genome or a TE database (a fasta file containing consensus sequences of TEs), are suitable for TE identification. ...
-
Build Securely on AWS with Proven FrameworksMoving to the cloud brings new challenges. How can you manage a larger attack surface while ensuring great network performance? Turn to Fortinet’s Tested Reference Architectures, blueprints for designing and securing cloud environments built by cybersecurity experts. Learn more and explore use cases in this white paper.
-
5
-
6
lemonade_assemble
Specialized sequence assembly tools
Assorted tools for: 1. Assembly of pooled BACs from PacBIO reads. 2. Polymorphic genome assembly 3. Processing of Trinity transcriptomes 4. Modified versions of other people's code used in any of the above. 5. Fasta processing and miscellaneous programs and scripts. Documentation is rudimentary or nonexistant. -
7
...The V4 version released here on SourceForge stay up as some automated release fetching packages rely on V4. MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.
-
8
○ Autoqc was developed to support platform-specific and automated quality control for beginners in metagenomics. ○ Autoqc supports simple and platform-specific quality control to efficiently decrease sequencing errors. For example, PacBio platform often produces long homopolymers, and Autoqc identifies lengths of homopolymers to remove erroneous reads for PacBio platform. ○ Autoqc supports automated quality control to maintain at least 60% of raw reads. For example, certain environmental samples may contain inhibitors, and bacterial DNA from them may not be totally pure. ...
-
9
BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.
-
Earn up to 16% annual interest with Nexo.Generate interest, access liquidity without selling, and execute trades seamlessly. All in one platform. Geographic restrictions, eligibility, and terms apply.
-
10
ETHA
Hybrid Illumina/PacBio assembly of Plasmodium falciparum var genes
ETHA is a software package for hybrid assembly of Plasmodium falciparum var genes from Illumina and PacBio sequencing data -
11
PBSuite
Software for Long-Read Sequencing Data from PacBio
.... ----- PBJelly ----- Read The Paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768 PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes. ----- PBHoney ----- Read The Paper http://www.biomedcentral.com/1471-2105/15/180/abstract PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). ... -
12
Opera
An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads. An updated version called OPERA-LG has been re-engineered with features for the assembly of large and complex genomes. Song Gao, Denis Bertrand, Burton K. H. Chia and Niranjan Nagarajan. OPERA-LG: efficient and exact scaffolding of large,... -
13
MuffinEC
Multi-technology, INDEL aware error correction for NGS data
MuffinEC is an error correction software capable of handling all types of errors (insertion deletions, mismatches and unknown bases). It officially supports four technologies (Illumina, 454, ion Torrent and PacBio - experimental) and it also has a generic setup for others (old and/or new). It is released under LGPL version 3.0. MuffinEC can use multicore systems, thanks to its OpenMP implementation. We are developing the 2nd version of MuffinEC. The beta version is already available online. The changes are listed in the VERSION_HISTORY file. ... -
14
Sparc: a consensus algorithm for PacBio/Nanopore data Manuscript can be found: https://peerj.com/preprints/1401.pdf
-
15
The Genome Mappability Analysis suite is used for measuring how well NGS reads can be mapped to reference genomes, especially for discovering variations
-
16
MLSTEZ is designed for next generation sequencing technology (PacBio CCS or Roche 454 platform) based MSLT methods. MLSTEZ, can automatically identify the barcodes and primers used in the PCR reaction, corrects sequencing errors, generates the MLST profile for each isolate, predicts the potential heterozygous locus, and outputs different alleles. Now ver2.0 supports asymmetric barcode design, please check manual for more details.
-
17
ReadSim
Simple reads simulator for pacbio & nanopore
Simple reads simulator for pacbio & nanopore -
18
caplib
Correct, translate and analyze combinatorial library sequencing data
Originally developped to handle PacBio CCS data for an AAV capsid library. This program will extract, correct, translate and analyze the sequencng data, starting from the CCS fastq file. -
19
Cerulean Hybrid Genome Assembler v0.1 Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. I am not able to maintain and update the software due to change in research funding. However I will be happy to answer any queries or provide support and comments if you are interested in extending this algorithm. The method is fully described in Deshpande, V., Fung, E. ...
- Previous
- You're on page 1
- Next
