Results for "FASTA"
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Comment on "REAPR: a universal tool for genome assembly evaluation"
...s are ok before we proceed! The command reapr facheck <assembly.fasta> will tell you if eve...ames. If you run into any problems, run reapr facheck <assembly.fasta> <renamed_assembly.fast...1516 days ago
- ...bsp; setGenome fasta|bam|genome &...
1700 days ago
Comment on "Perl script to count number of Ns in a multifasta file !"
If you want to count all 'N' in miltifasta file. (base) ? output_2_test git:(master) ? more scaffolds.fasta | grep -Ho N * | uniq -...sp; 12 draft_summary.info:N 1035948 scaffolds.fasta:N 12 sca...1743 days ago
Comment on "Extract fasta sequence from a multifasta file with fasta header Ids"
perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file If you have a large number o...'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' ids.file fasta.file...2090 days ago
Comment on "HALC: High throughput algorithm for long read error correction"
Inputs Long reads in FASTA format. Contigs assembled from the corresponding short reads in FASTA format. The initial short re...2271 days ago
- ...example: canu -d run1 -p godzilla genomeSize=1g -nanopore-raw reads/*.fasta.gz To restrict canu to only...plied in an optional sepc file with the -s option. Reads can be either FASTA or FASTQ format, uncompressed...
2278 days ago
Comment on "Installing Porechop on Ubuntu !"
➜ MyPassport porechop -i /media/urbe/MyDDrive/ONTdata/allONT/allONT.fasta -t 40 > ONT_choppedNcorrected.fa Loading reads/media/urbe/MyDDrive/ONTdata/allONT/allONT.fasta1,634,477 reads loaded Lookin...2285 days ago
- ...lp page -r <value>, --ref <value> an input reference file (fasta/fastq)[.gz] --refList <va...per line -q <value>, --query <value> an input query file (fasta/fastq)[.gz] --ql <value&g...
2302 days ago
- ...ty, sequencing depth, strand specificity, GC bias, read distribution over the genome structure and coverage uniformity. The input can be SAM, BAM, FASTA, BED files or Chromosome size...
2317 days ago
Comment on "Run miniasm assembler on nanopore reads !"
..._cat.fastq /home/data/20170911_minimap2_pacbio_oly.paf > /home/data/20170918_oly_pacbio_miniasm_reads.gfa 3 Convert miniasm output GFA to FASTA The FASTA file is needed to re-run mini...2347 days ago
