Results for "Fastq"
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Comment on "A quick guide to Phred scaling"
...quality scores are typically encoded in the quality score field of the FASTQ file format, which is a commo...h base call and are typically encoded in the quality score field of the FASTQ file format....403 days ago
Comment on "Short-read assembly using Spades !"
.... This step can be performed using various tools such as Trimmomatic or FastQC. Running SPAdes: After...is usually as follows: spades.py -o output_directory -1 forward_reads.fastq -2 reverse_reads.fastq Here,...403 days ago
Comment on "Short-read assembly using Spades !"
...ating systems. Prepare the input data: The input data should be in FASTQ format, which contains the se...tored. Then, enter the following command: spades.py -1 <read1.fastq> -2 <read2.fastq> -o...409 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...t \ ../../trimming_practical/nanofilt/nanofilt_trimmed.fastq \ ../../trimming_practical/nanofilt/nanofilt_trimmed.fastq \ | gzip -1 > ./minimap.p...-f \ ../../trimming_practical/nanofilt/nanofilt_trimmed.fastq \ ./minimap.paf.gz > mini...784 days ago
Comment on "URMAP, an ultra-fast read mapper"
...l FASTA file for the reference is not needed. Reads must be in FASTQ format or gzip-compressed FASTQ format. It is generally faste...e urmap attempts to create the file. Example urmap -map reads.fastq -ufi hg38.ufi -samout reads.s...1271 days ago
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
...reads into a single file, for gzipped files, this can be done with zcat, or for unzipped files cat. Ex. $ cat reads_R1.fastq >> combined.fastq $ zcat reads_R2.fastq.gz >...1325 days ago
- ...e is paired-end and requires an even number of FASTQ files represented as pairs, e...kallisto quant -i index -o output pairA_1.fastq pairA_2.fastq pairB_1.fastq p...d -s options, and list any number of FASTQ files, e.g kallisto quan...
1349 days ago
Comment on "Estimate Genome Size"
...documentation for options) gzip -dc reads1.fastq.gz reads2.fastq.gz | jellyfish count -m 31 -o.../0 # generate a histogram jellyfish histo fastq.counts_0 > fastq.counts_0....p pinpoint the actual peak find_valleys.pl fastq.counts_0.histo # estimate th...1886 days ago
- ...of options can be printed with '-options'. All options can be supplied in an optional sepc file with the -s option. Reads can be either FASTA or FASTQ format, uncompressed, or comp...
2087 days ago
Comment on "LAMSA: fast split read alignment with long approximate matches"
...nimum length of gap that causes a split-alignment. [100] -S --soft-clip Use soft clipping for supplementary alignment. [false] -C --comment Append FASTQ comment to SAM output. [false...2111 days ago
