Create some data

Let's create some dummy files to work with. Three samples (id1, id2, id3), paired end (R1, R2), split over four lanes (L001, L002, L003, L004).

touch id{1,2,3}_L00{1,2,3,4}_R{1,2}_001.fastq.gz
ls *.fastq.gz

id1_L001_R1_001.fastq.gz
id1_L001_R2_001.fastq.gz
id1_L002_R1_001.fastq.gz
id1_L002_R2_001.fastq.gz
id1_L003_R1_001.fastq.gz
id1_L003_R2_001.fastq.gz
id1_L004_R1_001.fastq.gz
id1_L004_R2_001.fastq.gz
id2_L001_R1_001.fastq.gz
id2_L001_R2_001.fastq.gz
id2_L002_R1_001.fastq.gz
id2_L002_R2_001.fastq.gz
id2_L003_R1_001.fastq.gz
id2_L003_R2_001.fastq.gz
id2_L004_R1_001.fastq.gz
id2_L004_R2_001.fastq.gz
id3_L001_R1_001.fastq.gz
id3_L001_R2_001.fastq.gz
id3_L002_R1_001.fastq.gz
id3_L002_R2_001.fastq.gz
id3_L003_R1_001.fastq.gz
id3_L003_R2_001.fastq.gz
id3_L004_R1_001.fastq.gz
id3_L004_R2_001.fastq.gz

Build a command

Let's find all the R1 read files, make sure they're in order, and line up the four lanes with paste.

find *R1*fastq.gz | sort | paste - - - -

id1_L001_R1_001.fastq.gz	id1_L002_R1_001.fastq.gz	id1_L003_R1_001.fastq.gz	id1_L004_R1_001.fastq.gz
id2_L001_R1_001.fastq.gz	id2_L002_R1_001.fastq.gz	id2_L003_R1_001.fastq.gz	id2_L004_R1_001.fastq.gz
id3_L001_R1_001.fastq.gz	id3_L002_R1_001.fastq.gz	id3_L003_R1_001.fastq.gz	id3_L004_R1_001.fastq.gz

Do this with R2 as well, and use process substitution to do it all in one fell swoop.

cat <(find *R1*fastq.gz | sort | paste - - - -) <(find *R2*fastq.gz | sort | paste - - - -) | sort

id1_L001_R1_001.fastq.gz	id1_L002_R1_001.fastq.gz	id1_L003_R1_001.fastq.gz	id1_L004_R1_001.fastq.gz
id1_L001_R2_001.fastq.gz	id1_L002_R2_001.fastq.gz	id1_L003_R2_001.fastq.gz	id1_L004_R2_001.fastq.gz
id2_L001_R1_001.fastq.gz	id2_L002_R1_001.fastq.gz	id2_L003_R1_001.fastq.gz	id2_L004_R1_001.fastq.gz
id2_L001_R2_001.fastq.gz	id2_L002_R2_001.fastq.gz	id2_L003_R2_001.fastq.gz	id2_L004_R2_001.fastq.gz
id3_L001_R1_001.fastq.gz	id3_L002_R1_001.fastq.gz	id3_L003_R1_001.fastq.gz	id3_L004_R1_001.fastq.gz
id3_L001_R2_001.fastq.gz	id3_L002_R2_001.fastq.gz	id3_L003_R2_001.fastq.gz	id3_L004_R2_001.fastq.gz

The next step uses GNU awk (from homebrew, gives you access to gensub). This bit will print the cat command, followed by the four read files you're concatenating, then a >, then prints out the first lane again, and substitutes out the stuff you don't need, and this is the output file name. It's easier to see what this does by looking at the result.

gawk '{ print "cat",$1,$2,$3,$4,">",gensub(/_L001_(R[12])_001/, "_\\1", "g", $1);}'

cat <(find *R1*fastq.gz | sort | paste - - - -) <(find *R2*fastq.gz | sort | paste - - - -) | sort | gawk '{ print "cat",$1,$2,$3,$4,">",gensub(/_L001_(R[12])_001/, "_\\1", "g", $1);}'

cat id1_L001_R1_001.fastq.gz id1_L002_R1_001.fastq.gz id1_L003_R1_001.fastq.gz id1_L004_R1_001.fastq.gz > id1_R1.fastq.gz
cat id1_L001_R2_001.fastq.gz id1_L002_R2_001.fastq.gz id1_L003_R2_001.fastq.gz id1_L004_R2_001.fastq.gz > id1_R2.fastq.gz
cat id2_L001_R1_001.fastq.gz id2_L002_R1_001.fastq.gz id2_L003_R1_001.fastq.gz id2_L004_R1_001.fastq.gz > id2_R1.fastq.gz
cat id2_L001_R2_001.fastq.gz id2_L002_R2_001.fastq.gz id2_L003_R2_001.fastq.gz id2_L004_R2_001.fastq.gz > id2_R2.fastq.gz
cat id3_L001_R1_001.fastq.gz id3_L002_R1_001.fastq.gz id3_L003_R1_001.fastq.gz id3_L004_R1_001.fastq.gz > id3_R1.fastq.gz
cat id3_L001_R2_001.fastq.gz id3_L002_R2_001.fastq.gz id3_L003_R2_001.fastq.gz id3_L004_R2_001.fastq.gz > id3_R2.fastq.gz

A script

The mergelanes.sh script in this repository will do this for you, echo'ing out all the commands you'll need to run.

./mergelanes.sh

cat id1_L001_R1_001.fastq.gz id1_L002_R1_001.fastq.gz id1_L003_R1_001.fastq.gz id1_L004_R1_001.fastq.gz > id1_R1.fastq.gz
cat id1_L001_R2_001.fastq.gz id1_L002_R2_001.fastq.gz id1_L003_R2_001.fastq.gz id1_L004_R2_001.fastq.gz > id1_R2.fastq.gz
cat id2_L001_R1_001.fastq.gz id2_L002_R1_001.fastq.gz id2_L003_R1_001.fastq.gz id2_L004_R1_001.fastq.gz > id2_R1.fastq.gz
cat id2_L001_R2_001.fastq.gz id2_L002_R2_001.fastq.gz id2_L003_R2_001.fastq.gz id2_L004_R2_001.fastq.gz > id2_R2.fastq.gz
cat id3_L001_R1_001.fastq.gz id3_L002_R1_001.fastq.gz id3_L003_R1_001.fastq.gz id3_L004_R1_001.fastq.gz > id3_R1.fastq.gz
cat id3_L001_R2_001.fastq.gz id3_L002_R2_001.fastq.gz id3_L003_R2_001.fastq.gz id3_L004_R2_001.fastq.gz > id3_R2.fastq.gz

Just pipe that to sh or parallel to run it.

./mergelanes.sh | sh

Limitations

It's not very flexible. You'll need to modify if you don't have paired end data, or if the read pairs are _1 and _2 instead of _R1 and _R2. It also assumes reads are split over four lanes. Again, easy to modify, but probably better to make the script more flexible. Contributions welcome.

An easier way?

Suggestion from Wei Shen:

cut is used to split id1_L001_R1_001.fastq.gz by _ to get the sample ID.

ls *R1* | cut -d _ -f 1 | sort | uniq \
    | while read id; do \
        cat $id*R1*.fastq.gz > $id.R1.fastq.gz;
        cat $id*R2*.fastq.gz > $id.R2.fastq.gz;
      done