Results for "fastq"
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KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...uite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The follo...filter: Filtering tools. Contains tools for filtering k-mer hashes and FastQ/A files: kmer: Produces a...1988 days ago
nanofilt: Filtering and trimming of long read sequencing data
Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and mapping https://github.com/wdecoster/nanofilt2112 days ago
- Read one or more FASTQ files, fastqe will compute quality stats for each file and print those stats as emoji... for some reason. Given a fastq file in Illumina 1.8+/Sanger format, calculate the mean (rounded) score for each position and print a corresponding emoji! https://fastqe.com/
2105 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
...and generate a core SNP alignment (and ultimately a phylogenomic tree). snippy --cpus 16 --outdir mysnps --ref Listeria.gbk --R1 FDA_R1.fastq.gz --R2 FDA_R2.fastq.gz2031 days ago
SimLoRD: A read simulator for third generation sequencing reads
...ormal distribution (typical for genomic DNA), sampling from an existing FASTQ file (typical for RNA), sampl...babilities are modified according to number of passes Outputs reads in FASTQ format and alignments in SAM...2089 days ago
SISRS: Site Identification from Short Read Sequences
Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads must have a fastq file extension.1991 days ago
PilonGrid: parallel wrapper around the Pilon framework
The distribution is a parallel wrapper around the Pilon framework The pipeline is composed of bash scripts, an example mapping.fofn which shows how to input your fastq files (you give paths to the R1 file), and how to launch the pipeline.1976 days ago
SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering...1938 days ago
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result,...1570 days ago
Sequanix: a dynamic graphical interface for Snakemake workflows
...na_coverage ease the extraction of genomic regions of interest and genome coverage information sequana_taxonomy performs a quick taxonomy of your FastQ. This requires dedicated data...1551 days ago
