Jit
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Libraries or management tools for high throughput sequencing data
Last updated 731 days ago by LEGEGATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.These methods enable the analysis of data sets of any size on multi-core desktop...Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
By Shruti Paniwala 2902 days agowww.well.ox.ac.uk - Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect...Classification of SARS-CoV2 Variant !
By Jit 1774 days agoThe scientists established some guidelines for determining whether a variant is a legitimate branch of an existing lineage:AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
By BioStar 3209 days agosourceforge.net - AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 2442 days agogenome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vttruvari: Structural variant comparison tool for VCFs
By Jit 2287 days agogithub.com - Structural variant comparison tool for VCFs Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure. Spiral Genetics MotivationvcfR
By Archana Malhotra 3699 days agocran.r-project.org - Most variant calling pipelines result in files containing large quantities of variant information. The variant call format (vcf) is an increasingly popular format for this data. The format of these files and their content is discussed in...Picard
By Neel 3811 days agobroadinstitute.github.io - Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 3056 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...-
sam to bam conversion !!
Last updated 3174 days ago by JitTo do sam to bam conversion, follow the following commands :- Code: $ samtools view -b -S file.sam > file.bam Then you will need to use Code: $ samtools sort file.bam file-sorted followed by Code: $ samtools index...
