UNICYCLER_POLISH(1)

📦 version 0.5.1, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

✨ UNICYCLER_POLISH(1) ✨

okay bestie, listen 💖 this is unicycler_polish, a lil User Command that does hybrid assembly polishing. yes it's giving "genomics girlboss" and yes I'm gonna walk you through every single flag, no skipping, periodt.

🦋 SYNOPSIS 🦋

unicycler_polish [-h] -a ASSEMBLY [-1 SHORT1] [-2 SHORT2] [--pb_bax
PB_BAX [PB_BAX ...]] [--pb_bam PB_BAM] [--pb_fasta PB_FASTA]
[--long_reads LONG_READS] [--no_fix_local] [--min_insert MIN_INSERT]
[--max_insert MAX_INSERT] [--min_align_length MIN_ALIGN_LENGTH]
[--homopolymer HOMOPOLYMER] [--large LARGE] [--illumina_alt
ILLUMINA_ALT] [--freebayes_qual_cutoff FREEBAYES_QUAL_CUTOFF] [--threads
THREADS] [--verbosity VERBOSITY] [--samtools SAMTOOLS] [--bowtie2
BOWTIE2] [--minimap2 MINIMAP2] [--freebayes FREEBAYES] [--pitchfork
PITCHFORK] [--bax2bam BAX2BAM] [--pbalign PBALIGN] [--arrow ARROW]
[--pilon PILON] [--java JAVA] [--ale ALE] [--racon RACON] [--minimap
MINIMAP] [--nucmer NUCMER] [--showsnps SHOWSNPS]

🌸 DESCRIPTION 🌸

Unicycler polish - hybrid assembly polishing 💅

that's it. that's the whole vibe. you give it an assembly, you give it some reads, it polishes. iconic.

🎀 OPTIONS 🎀

  • -h, --help — shows this help message and then dips. bye! 👋

🧬 Assembly

  • -a ASSEMBLY, --assembly ASSEMBLY — the input assembly that's getting polished. the main character, honestly 👑

🍓 Short reads

if you wanna polish with short reads (using Pilon), you gotta hand over two FASTQ files of paired-end reads. both of them. no solo acts.

  • -1 SHORT1, --short1 SHORT1 — FASTQ file of short reads (the first reads in each pair) 💖
  • -2 SHORT2, --short2 SHORT2 — FASTQ file of short reads (the second reads in each pair) 💖

🌈 PacBio reads

if you wanna polish with PacBio reads (using Arrow), give one of these lil guys:

  • --pb_bax PB_BAX [PB_BAX ...] — PacBio raw bax.h5 read files
  • --pb_bam PB_BAM — PacBio BAM read file
  • --pb_fasta PB_FASTA — FASTA file of PacBio reads

🧚 Generic long reads

if you wanna polish with generic long reads, hand over this one:

  • --long_reads LONG_READS — FASTQ/FASTA file of long reads

⭐ Polishing settings

a whole bunch of knobs for how the polishing behaves. lowkey the defaults should work great in most cases, so don't go feral unless you need to.

  • --no_fix_local — do not fix local misassemblies (default: False)
  • --min_insert MIN_INSERT — minimum valid short read insert size (default: auto)
  • --max_insert MAX_INSERT — maximum valid short read insert size (default: auto)
  • --min_align_length MIN_ALIGN_LENGTH — Minimum long read alignment length (default: 1000)
  • --homopolymer HOMOPOLYMER — Long read polish changes to a homopolymer of this length or greater will be ignored (default: 4)
  • --large LARGE — Variants of this size or greater will be assess as large variants (default: 10)
  • --illumina_alt ILLUMINA_ALT — When assessing long read changes with short read alignments, a variant will only be applied if the alternative occurrences in the short read alignments exceed this percentage (default: 5)
  • --freebayes_qual_cutoff FREEBAYES_QUAL_CUTOFF — Reject Pilon substitutions from long reads if the FreeBayes quality is less than this value (default: 10.0)

💜 Other settings

  • --threads THREADS — CPU threads to use in alignment and consensus (default: number of CPUs)
  • --verbosity VERBOSITY — Level of stdout information (0 to 3, default: 2) — 0 = no stdout, 1 = basic progress indicators, 2 = extra info, 3 = debugging info

🔧 Tool locations

if these required tools aren't chillin' in your PATH variable, just tell it where they live. and ngl, depending on which input reads you're using, some of these tools might not even be required, so no stress 💅

  • --samtools SAMTOOLS — path to samtools executable (default: samtools)
  • --bowtie2 BOWTIE2 — path to bowtie2 executable (default: bowtie2)
  • --minimap2 MINIMAP2 — path to minimap2 executable (default: minimap2)
  • --freebayes FREEBAYES — path to freebayes executable (default: freebayes)
  • --pitchfork PITCHFORK — Path to Pitchfork installation of PacBio tools (should contain bin and lib directories) (default: )
  • --bax2bam BAX2BAM — path to bax2bam executable (default: bax2bam)
  • --pbalign PBALIGN — path to pbalign executable (default: pbalign)
  • --arrow ARROW — path to arrow executable (default: arrow)
  • --pilon PILON — path to pilon jar file (default: pilon*.jar)
  • --java JAVA — path to java executable (default: java)
  • --ale ALE — path to ALE executable (default: ALE)
  • --racon RACON — path to racon executable (default: racon)
  • --minimap MINIMAP — path to miniasm executable (default: minimap)
  • --nucmer NUCMER — path to nucmer executable (default: nucmer)
  • --showsnps SHOWSNPS — path to show-snps executable (default: show-snps)
ok also tiny heads up: --pitchfork has an empty default, so if you need it you definitely gotta set it yourself. no cap.

👀 SEE ALSO 👀

💖 AUTHOR 💖

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. ty Andreas, we appreciate you 🫶

and that's the whole thing, bestie!! this was unicycler_polish version 0.4.7 from way back in October 2018 ✨ go forth and polish, you absolute icon 💅👑🌸

📦 where this page comes from