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Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Rahul Nayak 2571 days agogithub.com - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq dataAfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good...IONiseR: tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer
By Jit 2561 days agowww.bioconductor.org - This package is intended to provide tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer. It includes a functions to generate a number plots for examining the statistics that we think will be useful for this...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 1744 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...Picard
By Neel 3134 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...
BBMap/BBTools package: Multipurpose tool designed for converting reads or other nucleotide data...
Last updated 2920 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...Mauve: a system for constructing multiple genome alignments in the presence of large-scale...
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By Robert M Willioms 2539 days agogithub.com - SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
By BioJoker 2192 days agogithub.com - lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads...
