Alternatives and similar repositories for pre-pe

Users that are interested in pre-pe are comparing it to the libraries listed below

• karel-brinda / samsift
  SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.
  ☆23Updated 7 years ago
• Transipedia / dekupl
  Exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.
  ☆15Updated 6 years ago
• jhhung / PEAT
  An ultra fast and accurate paired-end adapter trimmer that needs no a priori adapter sequences.
  ☆22Updated 4 years ago
• jkbonfield / crumble
  Exploration of controlled loss of quality values for compressing CRAM files
  ☆34Updated 2 years ago
• hsinnan75 / MapCaller
  MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
  ☆30Updated 4 years ago
• rcedgar / urmap
  URMAP ultra-fast read mapper
  ☆39Updated 4 years ago
• ruolin / strawberry
  A program for fast and accurate genome-guided transcripts reconstruction and quantification from RNA-seq (Supporting Pacbio single-end)
  ☆23Updated 4 years ago
• jengelmann / FastqPuri
  fastq quality assessment and filtering tool
  ☆18Updated 2 years ago
• ksahlin / ultra
  Long-read splice alignment with high accuracy
  ☆63Updated 8 months ago
• lh3 / etrf
  Exact Tandem Repeat Finder (not a TRF replacement)
  ☆49Updated 5 years ago
• mikolmogorov / pbclip
  A simple tool to fix PacBio fasta/q that was not properly split into subreads
  ☆15Updated 3 years ago
• aquaskyline / 16GT
  Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
  ☆27Updated last year
• ryanlayer / svv
  Stupid Simple Structural Variant View
  ☆25Updated 8 years ago
• kamimrcht / REINDEER
  REINDEER REad Index for abuNDancE quERy
  ☆58Updated 10 months ago
• karel-brinda / ococo
  Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
  ☆47Updated 6 years ago
• telatin / covtobed
  ⛰ covtobed | Convert the coverage track from a BAM file into a BED file
  ☆44Updated 3 years ago
• jts / bri
  Bam Read Index - Extract alignments from a bam file by readname
  ☆25Updated last year
• brwnj / covviz
  Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
  ☆56Updated 3 years ago
• czc / nb_distribution
  novoBreak: local assembly for breakpoint detection in cancer genomes
  ☆26Updated 7 years ago
• ssadedin / ximmer
  Ximmer is a system for CNV calling on exome and targeted genomic sequencing
  ☆19Updated 3 months ago
• COMBINE-lab / RapClust
  Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes
  ☆31Updated 11 months ago
• kehrlab / PopDel
  Population-wide Deletion Calling
  ☆35Updated last month
• lh3 / htsbox
  My experimental tools on top of htslib. NOT OFFICIAL!!!
  ☆55Updated last year
• gzhmat / ShinyCNV
  a Shiny/R application to view and annotate copy number variations
  ☆27Updated 2 years ago
• DecodeGenetics / popSTR
  PopSTR - A Population based microsatellite genotyper
  ☆33Updated last year
• lh3 / sdust
  Symmetric DUST for finding low-complexity regions in DNA sequences
  ☆42Updated last year
• scottgigante / haplotyped-methylome
  Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation
  ☆23Updated 6 years ago
• langmead-lab / reference_flow
  Reducing reference bias using multiple population reference genomes
  ☆32Updated last year
• aganezov / RCK
  RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes
  ☆17Updated 5 years ago
• jmonlong / sveval
  Functions to compare a SV call sets against a truth set.
  ☆29Updated last year