Description

Scaffold a set of assemblies using YaHS and RagTag. YaHS is used to scaffold the first provided assembly, and then RagTag is used to scaffold the remaining assemblies using the first scaffolded assembly as a reference. Finally the RagTag scaffolds are re-scaffolded using YaHS to correct errors.

Input

Name
Description
Pattern

ch_fasta (file)

Channel containing assemblies for scaffolding. Structure: [ val(meta), path(fasta) ]

*.{bam/cram/sam}

ch_hic_bam (file)

Channel containing BAM files of Hi-C reads mapped to each assembly. Structure: [ val(meta), path(bam) ]

*.{bam/cram/sam}

Output

Name
Description
Pattern

scaffolds_fasta (file)

Final scaffolds from YaHS in FASTA format Structure: [ val(meta), path(fasta) ]

*.fasta

scaffolds_agp (file)

AGP describing how contigs are transformed into final scaffolds Structure: [ val(meta), path(agp) ]

*.agp

scaffolds_pairs (file)

Pairs file describing Hi-C contacts between scaffolds, translated from the contigs pairs file Structure: [ val(meta), path(pairs) ]

*.pairs.gz

scaffolds_chromsizes (file)

Chromsizes file for the scaffolds. A headerless TSV of format <contigname>\t<size> Structure: [ val(meta), path(chromsizes) ]

*.sizes

ragtag_scaffolds (file)

FASTA file of scaffolds output by RagTag Structure: [ val(meta), path(fasta) ]

*.fasta.gz

ragtag_agp (file)

AGP file describing how contigs are transformed into scaffolds by RagTag Structure: [ val(meta), path(agp) ]

*.agp

ragtag_stats (file)

Numerical genome statistics of RagTag scaffolds Structure: [ val(meta), path(agp) ]

*.stats

ragtag_paf (file)

PAF file describing alignments of contigs to the reference assembly by RagTag Structure: [ val(meta), path(paf) ]

*.paf.gz

ragtag_delta (file)

Nucmer DELTA file of alignments of contigs to the reference assembly by RagTag if using Nucmer aligner Structure: [ val(meta), path(agp) ]

*.delta.gz

confidence_txt (file)

Confidence scores used in scaffolding by RagTag Structure: [ val(meta), path(txt) ]

*.confidence.txt

yahs_bin (file)

YaHS binary file describing Hi-C contacts Structure: [ val(meta), path(bin) ]

*.bin

yahs_initial (file)

AGP files describing inital breaks by YaHS Structure: [ val(meta), path(agp) ]

*.agp

yahs_intermediate (file)

AGP files describing each scaffolding round by YaHS Structure: [ val(meta), path(agp) ]

*.agp

yahs_log (file)

YaHS log file Structure: [ val(meta), path(log) ]

*.log

Components

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