Results for "Read"
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Comment on "A quick guide to Phred scaling"
...r representing the quality scores of sequencing reads. It is used to quantify the...y of an error in each base call in a sequencing read. Here is a quick guide to Phr...is a common format used for storing sequencing reads. Each quality score is repre...406 days ago
Comment on "Short-read assembly using Spades !"
...pular software tool for short-read assembly. Here are the genera...ortant to ensure that the raw reads are of high quality and do n...o output_directory -1 forward_reads.fastq -2 reverse_reads.fastq...e the general steps for short-read assembly using SPAdes. Howeve...406 days ago
- ...The ART (short for Artificial Read Simulator) is a popular tool...that allows users to simulate reads with different error rates,...g technology. It can simulate reads with different read lengths,...dwgsim: dwgsim is a short read simulator that can generate s...
406 days ago
Comment on "Short-read assembly using Spades !"
...me assembler) is a popular tool for short-read assembly. It can assemble reads generated from Illumina, Ion...f overview of how to use SPAdes for short-read assembly: Install SPAdes...STQ format, which contains the sequencing reads. If the reads are paired-end...412 days ago
Comment on "CovCal: Coverage / Read Count Calculator"
...verage is defined as the average number of reads that covers each base of the...verage G is the length of the genome L is the read length N is the number of re...ngth 5Mbp and you simulate 1,000,000 HiSeq 2000 reads (read length is 100bp), then...574 days ago
Comment on "Far Manager Commands and Links !"
KeyDescription F1 Yes! Read it first. BTW, FarEng.hlf is a simple text file, you can open it in any editor. ShiftF1 Create new archive from selected f...952 days ago
Comment on "List of non-commercial NGS genotype-calling software"
Delly – Structural variant discovery by integrated paired-end and split-read analysis. [ paper-2012 ] lumpy – lumpy: a general probabilistic framewor...1133 days ago
Comment on "URMAP, an ultra-fast read mapper"
...the reference is not needed. Reads must be in FASTQ format or g...ly faster to use uncompressed reads because decompression is typ...get input from a pipe. If the reads are gzip-compressed, the fil...he file. Example urmap -map reads.fastq -ufi hg38.ufi -samout...1274 days ago
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
...ntent of the assembly compared to the kmer content of the read set. The first thing we need to do is to combine the reads into a single file, for gzip...he program, then create a comparison between the combined reads and the assembly. Make sure...1328 days ago
Comment on "REAPR: a universal tool for genome assembly evaluation"
...ssembly based on incongruently mapped reads. It is heavily based on too low span coverage, or reads mapping too far or too close...s a list of all “perfect” reads. This is reads that have a p...tmap which creates a bam file of read-pair mappings. Do the same th...1328 days ago
