BBTools for bioinformatician !
...nknown primers Code: $ reformat.sh in=reads.fq out=trimmed.fq ftr=19 This will trim all but the first 20 bases (a...ra.fa.gz" and get them all (this will increase the amount of overtrimming, though it should still b...2285 days ago
2148 days ago
CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
...line which runs in four steps: Detect overlaps in high-noise sequences using MHAP Generate corrected sequence consensus Trim corrected sequences Assemble trimmed corrected sequences Rea...2929 days ago
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
...INT: kmer_length (<=32, default: 23) -od STRING: output_file_directory (default: ./) -t INT: number of threads to use (default: 1) -trim : allow trimming (default: false) -maxco...1566 days ago
2729 days ago
Gap filling or Contigs extensions tools !
...ired reads that align extending these new paired-end reads. c. Construct a new assembly C' from C and the new reads identified in (a) and (b). d. Trim C' so it does not extend more...2180 days ago
Perl script to extract fasta sequence by matching name/ids !!
#!/usr/bin/perl use strict; use warnings; use Text::Trim qw(trim); #Usage perl extractSeqbyID.pl ids.txt...pen OUT, ">$out" or die; open FILE, "$fasta" or die; while () { trim($_); s/>//g; my ($i...2890 days ago
Installing Porechop on Ubuntu !
...[--require_two_barcodes] [--untrimmed] [--discard_unassigned]...] [--end_size END_SIZE] [--min_trim_size MIN_TRIM_SIZE]...(default: 4) --extra_end_trim EXTRA_END_TRIM...2121 days ago
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