diff --git a/DESCRIPTION b/DESCRIPTION
index 092b02f..08714df 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tzara
 Type: Package
 Title: Cluster long amplicons using dada2 denoising on variable regions
-Version: 0.0.7.3
+Version: 0.0.7.5
 Authors@R: person(given = "Brendan", family = "Furneaux",
                   email = "brendan.furneaux@gmail.com",
                   role = c("aut", "cre"))
@@ -50,4 +50,4 @@ Suggests:
     testthat (>= 2.1.0),
     covr,
     lintr
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.0
diff --git a/NAMESPACE b/NAMESPACE
index 07f742d..34bd8bd 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -8,6 +8,7 @@ S3method(dadamap,derep)
 S3method(dadamap,list)
 S3method(extract_region,ShortRead)
 S3method(extract_region,character)
+S3method(extract_region,list)
 S3method(seqhash,XStringSet)
 S3method(seqhash,character)
 S3method(summarize_sread,ShortReadQ)
diff --git a/R/tzara.R b/R/tzara.R
index 19c7d08..4f4e267 100644
--- a/R/tzara.R
+++ b/R/tzara.R
@@ -96,11 +96,13 @@ combine_derep <- function(dereps, .data = NULL, ...) {
    # preserve the sequence names as "seq.id" if they are present
    oldmap <- dereps
    oldmap[["oldmap"]] <- lapply(oldmap[["derep"]], `[[`, "map")
+   nestedcols <- "oldmap"
    if (all(vapply(oldmap[["derep"]], assertthat::has_name, TRUE, "names"))) {
       oldmap[["seq.id"]] <- lapply(oldmap[["derep"]], `[[`, "names")
+      nestedcols <- c(nestedcols, "seq.id")
    }
    oldmap <- dplyr::select(oldmap, -"derep") %>%
-      tidyr::unnest() %>%
+      tidyr::unnest(cols = nestedcols) %>%
       dplyr::group_by_at(gps) %>%
       dplyr::mutate(idx = 1:dplyr::n()) %>%
       dplyr::ungroup()
@@ -110,7 +112,7 @@ combine_derep <- function(dereps, .data = NULL, ...) {
       dplyr::mutate_at("derep",
                        ~purrr::map(., .f = ~tibble(seq = names(.$uniques),
                                                            n = .$uniques))) %>%
-      tidyr::unnest()
+      tidyr::unnest(cols = "derep")
 
    # combine duplicate sequences among all files.
    newuniques <- olduniques %>%
@@ -129,7 +131,7 @@ combine_derep <- function(dereps, .data = NULL, ...) {
          dplyr::mutate(oldmap = seq_along(seq)) %>%
          dplyr::ungroup(),
       newuniques,
-      .by = "seq")
+      by = "seq")
    }
 
    out <- list()
@@ -701,6 +703,8 @@ extract_region.ShortRead <- function(seq, positions, region, region2 = region,
    return(out)
 }
 
+#' @rdname extract_region
+#' @export
 extract_region.list <- function(seq, positions, region, region2 = region,
                                      outfile = NULL, ...) {
 
diff --git a/man/cluster_consensus.Rd b/man/cluster_consensus.Rd
index c71a481..fe439d6 100644
--- a/man/cluster_consensus.Rd
+++ b/man/cluster_consensus.Rd
@@ -8,11 +8,16 @@
 \usage{
 cluster_consensus(seq, ..., ncpus = 1, simplify = TRUE)
 
-\method{cluster_consensus}{character}(seq, names = names(seq),
-  dna2rna = TRUE, ..., ncpus = 1, simplify = TRUE)
+\method{cluster_consensus}{character}(
+  seq,
+  names = names(seq),
+  dna2rna = TRUE,
+  ...,
+  ncpus = 1,
+  simplify = TRUE
+)
 
-\method{cluster_consensus}{XStringSet}(seq, ..., ncpus = 1,
-  simplify = TRUE)
+\method{cluster_consensus}{XStringSet}(seq, ..., ncpus = 1, simplify = TRUE)
 }
 \arguments{
 \item{seq}{(\code{character} vector or \code{\link[Biostrings]{XStringSet}})
diff --git a/man/extract_region.Rd b/man/extract_region.Rd
index b6edab5..a83c5ca 100644
--- a/man/extract_region.Rd
+++ b/man/extract_region.Rd
@@ -4,17 +4,33 @@
 \alias{extract_region}
 \alias{extract_region.character}
 \alias{extract_region.ShortRead}
+\alias{extract_region.list}
 \title{Extract regions from a set of sequences (maybe with qualities)}
 \usage{
-extract_region(seq, positions, region, region2 = region,
-  outfile = NULL, ...)
+extract_region(seq, positions, region, region2 = region, outfile = NULL, ...)
 
-\method{extract_region}{character}(seq, positions, region,
-  region2 = region, outfile = NULL, qualityType = "FastqQuality",
-  append = FALSE, ...)
+\method{extract_region}{character}(
+  seq,
+  positions,
+  region,
+  region2 = region,
+  outfile = NULL,
+  qualityType = "FastqQuality",
+  append = FALSE,
+  ...
+)
 
-\method{extract_region}{ShortRead}(seq, positions, region,
-  region2 = region, outfile = NULL, append = FALSE, ...)
+\method{extract_region}{ShortRead}(
+  seq,
+  positions,
+  region,
+  region2 = region,
+  outfile = NULL,
+  append = FALSE,
+  ...
+)
+
+\method{extract_region}{list}(seq, positions, region, region2 = region, outfile = NULL, ...)
 }
 \arguments{
 \item{seq}{(\code{character} (a file name) or a
diff --git a/man/find_all_region_chimeras.Rd b/man/find_all_region_chimeras.Rd
index 8e30d2c..e3186aa 100644
--- a/man/find_all_region_chimeras.Rd
+++ b/man/find_all_region_chimeras.Rd
@@ -4,8 +4,14 @@
 \alias{find_all_region_chimeras}
 \title{Find chimeras in adjacent variable-conserved-variable domain triplets}
 \usage{
-find_all_region_chimeras(region_table, order, sample_column = NULL,
-  read_column = "read_id", chimera_offset = 0, ...)
+find_all_region_chimeras(
+  region_table,
+  order,
+  sample_column = NULL,
+  read_column = "read_id",
+  chimera_offset = 0,
+  ...
+)
 }
 \arguments{
 \item{region_table}{(\code{data.frame} containing all the regions in
diff --git a/man/find_region_chimeras.Rd b/man/find_region_chimeras.Rd
index db046ad..e360581 100644
--- a/man/find_region_chimeras.Rd
+++ b/man/find_region_chimeras.Rd
@@ -4,8 +4,7 @@
 \alias{find_region_chimeras}
 \title{Check for bimeras in a subset of regions}
 \usage{
-find_region_chimeras(region_table, chimset, sample_column, read_column,
-  ...)
+find_region_chimeras(region_table, chimset, sample_column, read_column, ...)
 }
 \arguments{
 \item{region_table}{(\code{data.frame} containing all the regions in
diff --git a/man/map_or_consensus.Rd b/man/map_or_consensus.Rd
index c336588..fefcfa9 100644
--- a/man/map_or_consensus.Rd
+++ b/man/map_or_consensus.Rd
@@ -4,8 +4,15 @@
 \alias{map_or_consensus}
 \title{Assign consensus sequences to unmapped reads}
 \usage{
-map_or_consensus(asvs, raw, maxdist = 10, allow_map = TRUE,
-  allow_consensus = TRUE, allow_raw = FALSE, ...)
+map_or_consensus(
+  asvs,
+  raw,
+  maxdist = 10,
+  allow_map = TRUE,
+  allow_consensus = TRUE,
+  allow_raw = FALSE,
+  ...
+)
 }
 \arguments{
 \item{asvs}{(\code{character} vector) ASV sequences mapped to a set of reads.
diff --git a/man/reconstruct.Rd b/man/reconstruct.Rd
index 388232c..7a62592 100644
--- a/man/reconstruct.Rd
+++ b/man/reconstruct.Rd
@@ -5,14 +5,28 @@
 \title{Reconstruct a longer region out of ASVs or consensus sequence of individual
 domains.}
 \usage{
-reconstruct(seqtabs, regions = names(seqtabs), regions_regex = NULL,
-  regions_replace = NULL, output = "concat", use_output = c("first",
-  "second", "no"), order = setdiff(regions, output),
-  read_column = "seq.id", asv_column = "dada.seq", rawtabs = seqtabs,
-  raw_column = NULL, raw_regions = names(rawtabs),
-  sample_column = NULL, sample_regex = NULL, sample_replace = NULL,
-  chimera_offset = 0, allow_map = TRUE, allow_consensus = TRUE,
-  allow_raw = FALSE, ...)
+reconstruct(
+  seqtabs,
+  regions = names(seqtabs),
+  regions_regex = NULL,
+  regions_replace = NULL,
+  output = "concat",
+  use_output = c("first", "second", "no"),
+  order = setdiff(regions, output),
+  read_column = "seq.id",
+  asv_column = "dada.seq",
+  rawtabs = seqtabs,
+  raw_column = NULL,
+  raw_regions = names(rawtabs),
+  sample_column = NULL,
+  sample_regex = NULL,
+  sample_replace = NULL,
+  chimera_offset = 0,
+  allow_map = TRUE,
+  allow_consensus = TRUE,
+  allow_raw = FALSE,
+  ...
+)
 }
 \arguments{
 \item{seqtabs}{(\code{list} of \code{data.frame}) with columns
diff --git a/man/seqhash.Rd b/man/seqhash.Rd
index 7f76a5b..65568b5 100644
--- a/man/seqhash.Rd
+++ b/man/seqhash.Rd
@@ -8,11 +8,9 @@
 \usage{
 seqhash(seq, algo = "xxhash32", len = NA, preserve_na = TRUE)
 
-\method{seqhash}{character}(seq, algo = "xxhash32", len = NA,
-  preserve_na = TRUE)
+\method{seqhash}{character}(seq, algo = "xxhash32", len = NA, preserve_na = TRUE)
 
-\method{seqhash}{XStringSet}(seq, algo = "xxhash32", len = NA,
-  preserve_na = TRUE)
+\method{seqhash}{XStringSet}(seq, algo = "xxhash32", len = NA, preserve_na = TRUE)
 }
 \arguments{
 \item{seq}{(\code{character} or \code{\link[Biostrings]{XStringSet}}) the