hicstuff

Arima-HiC mapping pipeline — shell-based workflow for aligning and processing Hi-C data generated with Arima Genomics proximity ligation kits. Maps paired-end FASTQ reads with BWA-MEM using Hi-C-speci

1 shared topic • 2 shared operations

distiller-nf — Nextflow pipeline for reproducible Hi-C data processing. Aligns Hi-C FASTQ reads with BWA, parses alignments into pairs with pairtools, filters PCR duplicates, and aggregates contacts i

1 shared topic • 2 shared operations

Fastq Screen — Perl tool for screening FASTQ sequencing reads against multiple reference genomes to detect sample contamination. Maps reads to user-defined genome databases (human, mouse, E. coli, Phi

1 shared topic • 2 shared operations

Mashtree — rapid distance-based phylogenetic tree construction from genome assemblies using MinHash (Mash) distances. Creates neighbor-joining trees from FASTA assemblies, FASTQ reads, or GenBank file

1 shared topic • 2 shared operations

Tools for manipulating next-generation sequencing data stored in SAM/BAM/CRAM format, including sorting, indexing, and format conversion.

1 shared topic • 2 shared operations