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...1379 days ago
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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...1605 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...1952 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...2134 days ago
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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...2148 days ago
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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...2209 days ago