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....432 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,...432 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...437 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...812 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...1300 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 >...1353 days ago
1377 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...1914 days ago
2115 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...2139 days ago