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BBMap/BBTools package: Multipurpose tool designed for converting reads or other nucleotide data...
Last updated 2918 days ago by JitReformat is a member of the BBMap/BBTools package. It is a multipurpose tool designed for converting reads or other nucleotide data between different formats. It supports, and can inter-convert: fastq fasta fasta+qual sam scarf (an old Illumina...Understanding PacBio
By Jitendra Narayan 2831 days agogithub.com - This tutorial includes resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts. Below are links to training modules (webinars and PowerPoint presentations) to help you...DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation...
By Jit 2777 days ago Comments (1)github.com - DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies Our work is published in Scientific Reports: Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous...NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
By Jit 2406 days ago Comments (1)github.com - CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2377 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
By Abhimanyu Singh 2271 days agowww.healthcare.uiowa.edu - Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added...FLAS: fast and high throughput algorithm for PacBio long read self-correction.
By Jit 1983 days agogithub.com - FLAS, a wrapper algorithm of MECAT, to achieve high throughput long read self-correction while keeping MECAT's fast speed. FLAS finds additional alignments from MECAT prealigned long reads to improve the correction throughput, and removes...Pacbio Long Reads Compatible Software and Tools
By Archana Malhotra 2811 days agogithub.com - The following software packages are known to be compatible with PacBio® data, in addition to PacBio's own SMRT® Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual...Cerulean: A hybrid assembly using high throughput short and long reads
By Rahul Nayak 2365 days agosourceforge.net - 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. The method is fully described in...
