Results for "reads"
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Comment on "A quick guide to Phred scaling"
...representing the quality scores of sequencing reads. It is used to quantify the p...is a common format used for storing sequencing reads. Each quality score is repres...representing the quality scores of sequencing reads, where higher scores indicate...405 days ago
Comment on "Short-read assembly using Spades !"
...quence from a large number of short sequencing reads. SPAdes (St. Petersburg genom...mbly using SPAdes: Quality control of raw reads: Before running the assembly,...ows: spades.py -o output_directory -1 forward_reads.fastq -2 reverse_reads.fastq...405 days ago
- ...ular tool for generating synthetic reads based on sequencing technolog...tool that allows users to simulate reads with different error rates, r...encing technology. It can simulate reads with different read lengths,...ulator that can generate synthetic reads from whole genome sequencing...
405 days ago
Comment on "Short-read assembly using Spades !"
...tool for short-read assembly. It can assemble reads generated from Illumina, IonT...in FASTQ format, which contains the sequencing reads. If the reads are paired-end,...s of the input files containing the paired-end reads, and <output_dir> with...411 days ago
Comment on "CovCal: Coverage / Read Count Calculator"
...erage is defined as the average number of reads that covers each base of the...nome L is the read length N is the number of reads For example, if you have a...gth 5Mbp and you simulate 1,000,000 HiSeq 2000 reads (read length is 100bp), then...573 days ago
Comment on "URMAP, an ultra-fast read mapper"
...the reference is not needed. Reads must be in FASTQ format or gz...ly faster to use uncompressed reads because decompression is typi...get input from a pipe. If the reads are gzip-compressed, the file...he file. Example urmap -map reads.fastq -ufi hg38.ufi -samout r...1273 days ago
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
...he first thing we need to do is to combine the reads into a single file, for gzipp...r for unzipped files cat. Ex. $ cat reads_R1.fastq >> combined.fa...then create a comparison between the combined reads and the assembly. Make sure t...1327 days ago
Comment on "REAPR: a universal tool for genome assembly evaluation"
...icit errors in the assembly based on incongruently mapped reads. It is heavily based on too low span coverage, or reads mapping too far or too close...ng we reapr needs, is a list of all “perfect” reads. This is reads that have a pe...1327 days ago
- kallisto can process either single-end or paired-end reads. The default running mode is paired-end and requires an even number of FASTQ files represented as pairs, e.g. kal...
1351 days ago
- ...nbsp; readsAsPairs [-on | -off] [-v] [tra...bsp; filterVariantReads [-r from/to] [-all] [-v] [tra...
1510 days ago
