Jit
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pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 3058 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...Postdoctoral Associate - Bioinformatics at Duke University Medical Center
The Department of Biostatistics and Bioinformatics at Duke University Medical Center is seeking a Postdoctoral Associate for a one year appointment to work on several high-dimensional research projects. The specific goals of the project are to...A-allele of SLC24A5 gene is found to be responsible for variation in skin color of South-East...
By Rahul Agarwal 4711 days agoMore is the A -allele, More is fairer the Skin !!Snippy: Rapid haploid variant calling and core SNP phylogeny
By Neel 2979 days agogithub.com - Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is...Variant Calling Pipeline
By LEGE 718 days agogithub.com - The variantcalling.nf nextflow script will take any number of samples with paired-end reads in FASTQ format, map reads using Bowtie2, process BAM files, and finally call variants using BCFtools v1.21 and/or Freebayes v1.3.6. If part of the...Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences
By Jit 3816 days agobioinformatics.ua.pt - Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For...DIAMOND
By Jit 3450 days agogithub.com - DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer...progressiveCactus
By Abhimanyu Singh 3429 days agogithub.com - Progressive Cactus is a whole-genome alignment package. Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules https://github.com/glennhickey/progressiveCactusSIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists
By Neel 3239 days agohciweb.iwr.uni-heidelberg.de - This is the c++ implementation for SIMA - Simultaneous Multiple Alignment of LC/MS Peak Lists. The package contains C++ source code as well as two binary files. The latter were tested under various operating systems, including Windows XP SP3 32bit,...LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
By Abhimanyu Singh 2952 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...
